{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Run stargeo queries for hetio-ind diseases" ] }, { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": false }, "outputs": [], "source": [ "import logging\n", "import os\n", "import gzip\n", "\n", "import pandas\n", "import easydict\n", "\n", "import starapi.analysis\n", "import starapi.conf" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [], "source": [ "starapi.analysis.logger.propagate = False\n", "starapi.conf.configure('data')" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
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slim_idslim_namecase_querycontrol_query
0DOID:0050156idiopathic pulmonary fibrosisIPF == 'IPF'IPF_control == 'IPF_control'
1DOID:0050741alcohol dependencealcoholism == 'alcoholism'alcoholism_control == 'alcoholism_control'
2DOID:0050742nicotine dependenceSmoker == 'Smoker'Smoker_control == 'Smoker_control'
3DOID:1024leprosyborderline_leprosy == 'borderline_leprosy' or ...leprosy_control == 'leprosy_control'
4DOID:10283prostate cancerPC == 'PC'PC_control == 'PC_control' or PC_tissue_contro...
\n", "
" ], "text/plain": [ " slim_id slim_name \\\n", "0 DOID:0050156 idiopathic pulmonary fibrosis \n", "1 DOID:0050741 alcohol dependence \n", "2 DOID:0050742 nicotine dependence \n", "3 DOID:1024 leprosy \n", "4 DOID:10283 prostate cancer \n", "\n", " case_query \\\n", "0 IPF == 'IPF' \n", "1 alcoholism == 'alcoholism' \n", "2 Smoker == 'Smoker' \n", "3 borderline_leprosy == 'borderline_leprosy' or ... \n", "4 PC == 'PC' \n", "\n", " control_query \n", "0 IPF_control == 'IPF_control' \n", "1 alcoholism_control == 'alcoholism_control' \n", "2 Smoker_control == 'Smoker_control' \n", "3 leprosy_control == 'leprosy_control' \n", "4 PC_control == 'PC_control' or PC_tissue_contro... " ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "query_df = pandas.read_table('data/queries.tsv')\n", "query_df.head()" ] }, { "cell_type": "code", "execution_count": 4, "metadata": { "collapsed": false, "scrolled": true }, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_0050156 analysis\n", "/home/dhimmels/anaconda3/envs/stargeo/lib/python2.7/site-packages/pandas/core/indexing.py:115: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame\n", "\n", "See the the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", " self._setitem_with_indexer(indexer, value)\n", "915.86 ms in get_analysis_df(\"IPF == 'IPF'\", \"IPF_control == 'IPF_c..., '')\n", "920.37 ms in Loading dataframe for DOID_0050156\n", "Matching sources: 12\n", "Stats: 12 sources, 12 series, 8 platforms, 679 samples\n", "Loading data and calculating fold change for DOID_0050156\n", "Loading data for GSE10667, id = 179\n", "733.09 ms in get_probes(10)\n", " 18.13 s in load_gse( series_id platform_id..., 179, False)\n", "/home/dhimmels/Documents/serg/rephetio/construct/star_api/starapi/analysis.py:168: SettingWithCopyWarning: \n", "A value is trying to be set on a copy of a slice from a DataFrame.\n", "Try using .loc[row_indexer,col_indexer] = value instead\n", "\n", "See the the caveats in the documentation: http://pandas.pydata.org/pandas-docs/stable/indexing.html#indexing-view-versus-copy\n", " samples['subset'] = \"NA\"\n", " 3.45 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17978, id = 2072\n", "621.34 ms in get_probes(593)\n", " 19.05 s in load_gse( series_id platform_id..., 2072, False)\n", " 3.02 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE2052, id = 2719\n", "279.66 ms in get_probes(687)\n", " 3.88 s in load_gse( series_id platform_id..., 2719, False)\n", " 1.04 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE24206, id = 3666\n", "626.52 ms in get_probes(4)\n", " 17.90 s in load_gse( series_id platform_id..., 3666, False)\n", " 3.33 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE28042, id = 4602\n", "524.96 ms in get_probes(53)\n", " 34.31 s in load_gse( series_id platform_id..., 4602, False)\n", " 5.57 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE28221, id = 4650\n", "506.39 ms in get_probes(53)\n", " 33.68 s in load_gse( series_id platform_id..., 4650, False)\n", " 5.80 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE31934, id = 5581\n", "111.77 ms in get_probes(1004)\n", "490.42 ms in load_gse( series_id platform_id..., 5581, False)\n", "453.72 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE33566, id = 5969\n", "544.43 ms in get_probes(53)\n", " 23.24 s in load_gse( series_id platform_id..., 5969, False)\n", " 4.69 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE35145, id = 6333\n", "526.27 ms in get_probes(674)\n", " 7.53 s in load_gse( series_id platform_id..., 6333, False)\n", " 1.94 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE38958, id = 7205\n", "539.93 ms in get_probes(280)\n", " 26.03 s in load_gse( series_id platform_id..., 7205, False)\n", " 6.33 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE45686, id = 8724\n", "526.17 ms in get_probes(674)\n", " 23.63 s in load_gse( series_id platform_id..., 8724, False)\n", " 3.25 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE53845, id = 12401\n", "696.20 ms in get_probes(53)\n", " 19.18 s in load_gse( series_id platform_id..., 12401, False)\n", " 3.15 s in get_gene_fold_change(, False, 0, None)\n", "273.18 s in Load/fold for DOID_0050156\n", "Meta-Analyzing DOID_0050156\n", "450.82 s in meta analysis of real data for DOID_0050156\n", "981.75 ms in meta analysis of permutations for DOID_0050156\n", "204.09 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "452.40 s in Meta analysis for DOID_0050156\n", "DONE DOID_0050156 analysis\n", "726.74 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "0 DOID:0050156 idiopathic pulmonary fibrosis\n", "1" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_0050741 analysis\n", "935.05 ms in get_analysis_df(\"alcoholism == 'alcoho..., \"alcoholism_control ==..., '')\n", "939.27 ms in Loading dataframe for DOID_0050741\n", "Matching sources: 8\n", "Stats: 8 sources, 8 series, 8 platforms, 435 samples\n", "Loading data and calculating fold change for DOID_0050741\n", "Loading data for GSE10356, id = 95\n", " 39.47 ms in get_probes(36)\n", " 22.10 s in load_gse( series_id platform_id..., 95, False)\n", "205.21 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20568, id = 2733\n", " 42.28 ms in get_probes(689)\n", " 2.34 s in load_gse( series_id platform_id..., 2733, False)\n", "324.24 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29555, id = 5002\n", "492.71 ms in get_probes(389)\n", " 21.88 s in load_gse( series_id platform_id..., 5002, False)\n", " 5.61 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE44456, id = 8480\n", "411.77 ms in get_probes(283)\n", " 12.21 s in load_gse( series_id platform_id..., 8480, False)\n", " 2.61 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE49376, id = 9395\n", "386.02 ms in get_probes(789)\n", " 11.28 s in load_gse( series_id platform_id..., 9395, False)\n", " 2.24 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE53808, id = 10083\n", "687.26 ms in get_probes(841)\n", " 16.98 s in load_gse( series_id platform_id..., 10083, False)\n", " 4.00 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE9058, id = 11639\n", " 42.36 ms in get_probes(1630)\n", " 3.00 s in load_gse( series_id platform_id..., 11639, False)\n", "366.50 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE52553, id = 12329\n", "628.57 ms in get_probes(4)\n", " 46.63 s in load_gse( series_id platform_id..., 12329, False)\n", " 6.93 s in get_gene_fold_change(, False, 0, None)\n", "161.31 s in Load/fold for DOID_0050741\n", "Meta-Analyzing DOID_0050741\n", "388.82 s in meta analysis of real data for DOID_0050741\n", "487.60 ms in meta analysis of permutations for DOID_0050741\n", "135.90 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "389.91 s in Meta analysis for DOID_0050741\n", "DONE DOID_0050741 analysis\n", "552.36 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:0050741 alcohol dependence\n", "2" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_0050742 analysis\n", " 1.08 s in get_analysis_df(\"Smoker == 'Smoker'\", \"Smoker_control == 'Sm..., '')\n", " 1.08 s in Loading dataframe for DOID_0050742\n", "Matching sources: 22\n", "Excluded 3 sources as single-class\n", "Stats: 19 sources, 17 series, 6 platforms, 1423 samples\n", "Loading data and calculating fold change for DOID_0050742\n", "Loading data for GSE10006, id = 4\n", "631.65 ms in get_probes(4)\n", " 45.85 s in load_gse( series_id platform_id..., 4, False)\n", " 7.15 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE11784, id = 450\n", "649.63 ms in get_probes(4)\n", " 85.42 s in load_gse( series_id platform_id..., 450, False)\n", " 11.72 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE11906, id = 487\n", "632.96 ms in get_probes(4)\n", "114.28 s in load_gse( series_id platform_id..., 487, False)\n", " 15.96 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE19407, id = 2430\n", "667.29 ms in get_probes(4)\n", " 64.76 s in load_gse( series_id platform_id..., 2430, False)\n", " 3.05 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20257, id = 2650\n", "479.26 ms in get_probes(4)\n", " 68.46 s in load_gse( series_id platform_id..., 2650, False)\n", " 10.23 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20568, id = 2733\n", " 42.03 ms in get_probes(689)\n", " 2.26 s in load_gse( series_id platform_id..., 2733, False)\n", "402.85 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27272, id = 4446\n", "444.34 ms in get_probes(331)\n", " 53.00 s in load_gse( series_id platform_id..., 4446, False)\n", " 6.65 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE30063, id = 5140\n", "629.17 ms in get_probes(4)\n", " 50.30 s in load_gse( series_id platform_id..., 5140, False)\n", "skipping GPL570: sample ids mismatch\n", "145.15 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE3320, id = 5880\n", "390.59 ms in get_probes(2)\n", " 3.95 s in load_gse( series_id platform_id..., 5880, False)\n", " 1.46 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE4498, id = 8585\n", "623.13 ms in get_probes(4)\n", " 16.09 s in load_gse( series_id platform_id..., 8585, False)\n", " 3.22 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5056, id = 9571\n", "220.70 ms in get_probes(22)\n", " 3.29 s in load_gse( series_id platform_id..., 9571, False)\n", "915.41 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5057, id = 9574\n", "392.47 ms in get_probes(2)\n", " 3.95 s in load_gse( series_id platform_id..., 9574, False)\n", " 1.39 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5058, id = 9577\n", "333.80 ms in get_probes(4)\n", " 21.69 s in load_gse( series_id platform_id..., 9577, False)\n", " 3.05 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5059, id = 9580\n", "448.12 ms in get_probes(4)\n", " 4.71 s in load_gse( series_id platform_id..., 9580, False)\n", " 1.18 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5060, id = 9582\n", "627.81 ms in get_probes(4)\n", "218.55 ms in get_probes(22)\n", "412.39 ms in get_probes(2)\n", " 39.71 s in load_gse( series_id platform_id..., 9582, False)\n", " 6.91 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6264, id = 10896\n", "411.24 ms in get_probes(78)\n", " 9.70 s in load_gse( series_id platform_id..., 10896, False)\n", " 1.75 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE8545, id = 11509\n", "654.10 ms in get_probes(4)\n", " 32.19 s in load_gse( series_id platform_id..., 11509, False)\n", " 5.14 s in get_gene_fold_change(, False, 0, None)\n", "706.43 s in Load/fold for DOID_0050742\n", "Meta-Analyzing DOID_0050742\n", "425.75 s in meta analysis of real data for DOID_0050742\n", " 1.65 s in meta analysis of permutations for DOID_0050742\n", "139.95 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "428.01 s in Meta analysis for DOID_0050742\n", "DONE DOID_0050742 analysis\n", "1135.78 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:0050742 nicotine dependence\n", "3" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_1024 analysis\n", " 1.30 s in get_analysis_df(\"borderline_leprosy ==..., \"leprosy_control == 'l..., '')\n", " 1.30 s in Loading dataframe for DOID_1024\n", "Matching sources: 1\n", "Excluded 1 source by min samples\n", "FAIL Can't perform meta-analysis on no data\n", " 1.45 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:1024 leprosy\n", "4" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_10283 analysis\n", "970.33 ms in get_analysis_df(\"PC == 'PC'\", \"PC_control == 'PC_con..., '')\n", "974.80 ms in Loading dataframe for DOID_10283\n", "Matching sources: 16\n", "Excluded 13 sources as single-class\n", "Stats: 3 sources, 3 series, 2 platforms, 464 samples\n", "Loading data and calculating fold change for DOID_10283\n", "Loading data for GSE11682, id = 437\n", "683.58 ms in get_probes(10)\n", " 21.18 s in load_gse( series_id platform_id..., 437, False)\n", " 3.14 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE30994, id = 5362\n", "691.05 ms in get_probes(10)\n", " 7.43 s in load_gse( series_id platform_id..., 5362, False)\n", " 1.85 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE62872, id = 13217\n", " 40.58 ms in get_probes(1787)\n", " 73.23 s in load_gse( series_id platform_id..., 13217, False)\n", "384.08 ms in get_gene_fold_change(, False, 0, None)\n", "108.32 s in Load/fold for DOID_10283\n", "Meta-Analyzing DOID_10283\n", "330.96 s in meta analysis of real data for DOID_10283\n", "222.74 ms in meta analysis of permutations for DOID_10283\n", "139.95 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper I..., Empty DataFrame Column...)\n", "331.84 s in Meta analysis for DOID_10283\n", "DONE DOID_10283 analysis\n", "441.33 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:10283 prostate cancer\n", "5" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_10534 analysis\n", "688.48 ms in get_analysis_df(\"stomach_cancer_tissue..., \"stomach_cancer_tissue..., '')\n", "692.69 ms in Loading dataframe for DOID_10534\n", "Matching sources: 2\n", "Excluded 1 source as single-class\n", "FAIL Can't perform meta-analysis on single source\n", "830.04 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:10534 stomach cancer\n", "6" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_10608 analysis\n", "602.89 ms in get_analysis_df(\"celiac == 'celiac'\", \"celiac_control == 'ce..., '')\n", "607.10 ms in Loading dataframe for DOID_10608\n", "Matching sources: 1\n", "FAIL Can't perform meta-analysis on single source\n", "741.56 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:10608 celiac disease\n", "7" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_10652 analysis\n", "698.75 ms in get_analysis_df(\"AD == 'AD'\", \"AD_Control == 'AD_Con..., '')\n", "703.39 ms in Loading dataframe for DOID_10652\n", "Matching sources: 4\n", "Excluded 2 sources as single-class\n", "Stats: 2 sources, 2 series, 2 platforms, 512 samples\n", "Loading data and calculating fold change for DOID_10652\n", "Loading data for GSE33000, id = 5836\n", "603.23 ms in get_probes(297)\n", "282.01 s in load_gse( series_id platform_id..., 5836, False)\n", " 17.46 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6613, id = 11004\n", "394.15 ms in get_probes(2)\n", " 18.90 s in load_gse( series_id platform_id..., 11004, False)\n", " 2.58 s in get_gene_fold_change(, False, 0, None)\n", "321.61 s in Load/fold for DOID_10652\n", "Meta-Analyzing DOID_10652\n", "204.31 s in meta analysis of real data for DOID_10652\n", "158.82 ms in meta analysis of permutations for DOID_10652\n", "132.08 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper I..., Empty DataFrame Column...)\n", "205.10 s in Meta analysis for DOID_10652\n", "DONE DOID_10652 analysis\n", "527.58 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:10652 Alzheimer's disease\n", "8" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_10763 analysis\n", "773.56 ms in get_analysis_df(\"PHT == 'PHT' or hyper..., \"PHT_Control == 'PHT_C..., '')\n", "777.83 ms in Loading dataframe for DOID_10763\n", "Matching sources: 8\n", "Excluded 1 source as single-class\n", "Stats: 7 sources, 7 series, 6 platforms, 309 samples\n", "Loading data and calculating fold change for DOID_10763\n", "Loading data for GSE10767, id = 202\n", "640.46 ms in get_probes(4)\n", " 7.93 s in load_gse( series_id platform_id..., 202, False)\n", " 2.33 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE15197, id = 1359\n", "501.87 ms in get_probes(53)\n", " 14.78 s in load_gse( series_id platform_id..., 1359, False)\n", " 2.62 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE19617, id = 2473\n", "677.07 ms in get_probes(53)\n", " 12.51 s in load_gse( series_id platform_id..., 2473, False)\n", " 2.48 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE24988, id = 3871\n", "420.34 ms in get_probes(283)\n", " 32.75 s in load_gse( series_id platform_id..., 3871, False)\n", " 3.82 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE33463, id = 5944\n", "487.04 ms in get_probes(389)\n", " 60.72 s in load_gse( series_id platform_id..., 5944, False)\n", " 5.80 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE48149, id = 9192\n", "410.54 ms in get_probes(1292)\n", " 10.33 s in load_gse( series_id platform_id..., 9192, False)\n", " 1.77 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE703, id = 11135\n", "213.02 ms in get_probes(22)\n", " 1.86 s in load_gse( series_id platform_id..., 11135, False)\n", "710.23 ms in get_gene_fold_change(, False, 0, None)\n", "163.00 s in Load/fold for DOID_10763\n", "Meta-Analyzing DOID_10763\n", "409.11 s in meta analysis of real data for DOID_10763\n", "551.80 ms in meta analysis of permutations for DOID_10763\n", "143.77 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "410.25 s in Meta analysis for DOID_10763\n", "DONE DOID_10763 analysis\n", "574.23 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:10763 hypertension\n", "9" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_10871 analysis\n", "848.31 ms in get_analysis_df(\"AMD == 'AMD'\", \"AMD_control == 'AMD_c..., '')\n", "852.83 ms in Loading dataframe for DOID_10871\n", "Matching sources: 1\n", "FAIL Can't perform meta-analysis on single source\n", "992.27 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:10871 age related macular degeneration\n", "10" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_1094 analysis\n", "527.38 ms in get_analysis_df(\"ADHD == 'ADHD'\", \"ADHD_control == 'ADHD..., '')\n", "531.70 ms in Loading dataframe for DOID_1094\n", "Matching sources: 1\n", "Excluded 1 source by min samples\n", "FAIL Can't perform meta-analysis on no data\n", "670.63 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:1094 attention deficit hyperactivity disorder\n", "11" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_11054 analysis\n", "187.60 ms in get_analysis_df(\"bladder_cancer == 'bl..., \"bladder_cancer_contro..., '')\n", "192.53 ms in Loading dataframe for DOID_11054\n", "Matching sources: 0\n", "FAIL Can't perform meta-analysis on no data\n", "257.00 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:11054 urinary bladder cancer\n", "12" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_11612 analysis\n", "659.71 ms in get_analysis_df(\"PCOS == 'PCOS'\", \"PCOS_control == 'PCOS..., '')\n", "663.94 ms in Loading dataframe for DOID_11612\n", "Matching sources: 11\n", "Stats: 11 sources, 10 series, 5 platforms, 215 samples\n", "Loading data and calculating fold change for DOID_11612\n", "Loading data for GSE10946, id = 254\n", "627.60 ms in get_probes(4)\n", " 18.10 s in load_gse( series_id platform_id..., 254, False)\n", " 2.58 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE1615, id = 1613\n", "394.39 ms in get_probes(2)\n", "328.87 ms in get_probes(50)\n", " 8.39 s in load_gse( series_id platform_id..., 1613, False)\n", " 2.51 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE34526, id = 6193\n", "633.63 ms in get_probes(4)\n", " 10.67 s in load_gse( series_id platform_id..., 6193, False)\n", " 2.53 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE43264, id = 8243\n", "352.05 ms in get_probes(1160)\n", " 4.34 s in load_gse( series_id platform_id..., 8243, False)\n", " 1.42 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE43322, id = 8252\n", "350.34 ms in get_probes(1160)\n", " 7.19 s in load_gse( series_id platform_id..., 8252, False)\n", " 1.71 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE48301, id = 9220\n", "404.42 ms in get_probes(283)\n", " 10.89 s in load_gse( series_id platform_id..., 9220, False)\n", " 2.17 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5090, id = 9638\n", "386.80 ms in get_probes(2)\n", " 4.76 s in load_gse( series_id platform_id..., 9638, False)\n", " 1.54 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5850, id = 10693\n", "620.85 ms in get_probes(4)\n", " 9.47 s in load_gse( series_id platform_id..., 10693, False)\n", " 2.61 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6798, id = 11053\n", "622.97 ms in get_probes(4)\n", " 18.75 s in load_gse( series_id platform_id..., 11053, False)\n", " 3.63 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE8157, id = 11431\n", "630.11 ms in get_probes(4)\n", " 31.07 s in load_gse( series_id platform_id..., 11431, False)\n", " 2.61 s in get_gene_fold_change(, False, 0, None)\n", "150.63 s in Load/fold for DOID_11612\n", "Meta-Analyzing DOID_11612\n", "424.83 s in meta analysis of real data for DOID_11612\n", "927.93 ms in meta analysis of permutations for DOID_11612\n", "133.99 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "426.36 s in Meta analysis for DOID_11612\n", "DONE DOID_11612 analysis\n", "577.86 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:11612 polycystic ovary syndrome\n", "13" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_11714 analysis\n", " 1.16 s in get_analysis_df(\"GDM == 'GDM'\", \"GDM_control == 'GDM_c..., '')\n", " 1.17 s in Loading dataframe for DOID_11714\n", "Matching sources: 4\n", "Excluded 2 sources by min samples\n", "Stats: 2 sources, 2 series, 2 platforms, 12 samples\n", "Loading data and calculating fold change for DOID_11714\n", "Loading data for GSE49524, id = 9415\n", "383.56 ms in get_probes(482)\n", " 3.80 s in load_gse( series_id platform_id..., 9415, False)\n", " 1.29 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE65737, id = 13510\n", " 39.08 ms in get_probes(1802)\n", " 7.65 s in load_gse( series_id platform_id..., 13510, False)\n", "259.91 ms in get_gene_fold_change(, False, 0, None)\n", " 13.24 s in Load/fold for DOID_11714\n", "Meta-Analyzing DOID_11714\n", "FAIL Got empty meta-analysis\n", " 24.41 s in meta analysis of real data for DOID_11714\n", " 24.41 s in Meta analysis for DOID_11714\n", " 38.99 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:11714 gestational diabetes\n", "14" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_11949 analysis\n", "683.39 ms in get_analysis_df(\"CJD == 'CJD'\", \"CJD_control == 'CJD_c..., '')\n", "688.06 ms in Loading dataframe for DOID_11949\n", "Matching sources: 1\n", "Excluded 1 source by min samples\n", "FAIL Can't perform meta-analysis on no data\n", "829.53 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:11949 Creutzfeldt-Jakob disease\n", "15" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_12306 analysis\n", "528.20 ms in get_analysis_df(\"vitiligo == 'vitiligo'\", \"vitiligo_control == '..., '')\n", "532.34 ms in Loading dataframe for DOID_12306\n", "Matching sources: 1\n", "FAIL Can't perform meta-analysis on single source\n", "665.96 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:12306 vitiligo\n", "16" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_12365 analysis\n", "772.40 ms in get_analysis_df(\"malaria == 'malaria'\", \"malaria_control == 'm..., '')\n", "776.55 ms in Loading dataframe for DOID_12365\n", "Matching sources: 8\n", "Excluded 1 source as single-class\n", "Excluded 1 source by min samples\n", "Stats: 6 sources, 6 series, 5 platforms, 295 samples\n", "Loading data and calculating fold change for DOID_12365\n", "Loading data for GSE15221, id = 1372\n", "472.48 ms in get_probes(17)\n", " 18.50 s in load_gse( series_id platform_id..., 1372, False)\n", " 2.54 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE18323, id = 2164\n", "504.85 ms in get_probes(9)\n", " 59.50 s in load_gse( series_id platform_id..., 2164, False)\n", " 2.99 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE24849, id = 3840\n", "665.61 ms in get_probes(4)\n", " 20.08 s in load_gse( series_id platform_id..., 3840, False)\n", " 3.15 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE34404, id = 6155\n", "622.84 ms in get_probes(674)\n", " 81.11 s in load_gse( series_id platform_id..., 6155, False)\n", " 9.39 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5418, id = 10145\n", "387.07 ms in get_probes(2)\n", " 15.67 s in load_gse( series_id platform_id..., 10145, False)\n", " 2.23 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE7586, id = 11293\n", "630.14 ms in get_probes(4)\n", " 12.58 s in load_gse( series_id platform_id..., 11293, False)\n", " 2.65 s in get_gene_fold_change(, False, 0, None)\n", "232.71 s in Load/fold for DOID_12365\n", "Meta-Analyzing DOID_12365\n", "427.04 s in meta analysis of real data for DOID_12365\n", "541.35 ms in meta analysis of permutations for DOID_12365\n", "127.08 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "428.18 s in Meta analysis for DOID_12365\n", "DONE DOID_12365 analysis\n", "661.86 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:12365 malaria\n", "17" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_12849 analysis\n", "972.66 ms in get_analysis_df(\"autism == 'autism'\", \"autism_control == 'au..., '')\n", "976.91 ms in Loading dataframe for DOID_12849\n", "Matching sources: 14\n", "Excluded 1 source as single-class\n", "Excluded 1 source by min samples\n", "Stats: 12 sources, 11 series, 7 platforms, 1302 samples\n", "Loading data and calculating fold change for DOID_12849\n", "Loading data for GSE15402, id = 1425\n", "574.85 ms in get_probes(497)\n", " 43.99 s in load_gse( series_id platform_id..., 1425, False)\n", " 4.44 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE15451, id = 1434\n", "611.95 ms in get_probes(497)\n", " 14.35 s in load_gse( series_id platform_id..., 1434, False)\n", " 2.13 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE18123, id = 2111\n", "621.44 ms in get_probes(4)\n", "409.51 ms in get_probes(283)\n", "116.39 s in load_gse( series_id platform_id..., 2111, False)\n", " 10.72 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE25507, id = 4004\n", "697.71 ms in get_probes(4)\n", " 90.69 s in load_gse( series_id platform_id..., 4004, False)\n", " 10.06 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE26415, id = 4204\n", "500.18 ms in get_probes(53)\n", " 17.25 s in load_gse( series_id platform_id..., 4204, False)\n", " 4.76 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE28521, id = 4729\n", "424.22 ms in get_probes(331)\n", " 10.15 s in load_gse( series_id platform_id..., 4729, False)\n", " 3.25 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE37772, id = 6963\n", "433.29 ms in get_probes(331)\n", "111.35 s in load_gse( series_id platform_id..., 6963, False)\n", " 15.74 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE38322, id = 7080\n", "528.52 ms in get_probes(674)\n", " 21.71 s in load_gse( series_id platform_id..., 7080, False)\n", " 3.01 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE43076, id = 8190\n", "513.79 ms in get_probes(53)\n", "891.11 ms in load_gse( series_id platform_id..., 8190, False)\n", "/home/dhimmels/anaconda3/envs/stargeo/lib/python2.7/site-packages/numpy/lib/nanfunctions.py:227: RuntimeWarning: All-NaN axis encountered\n", " warnings.warn(\"All-NaN axis encountered\", RuntimeWarning)\n", " 1.93 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE42133, id = 12084\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:12849 autistic disorder\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE42133/GSE42133_series_matrix.txt.gz ...\n", "Cache to" ] }, { "name": "stderr", "output_type": "stream", "text": [ "541.31 ms in get_probes(674)\n", " 86.31 s in load_gse( series_id platform_id..., 12084, False)\n", " 7.93 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE63524, id = 13274\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " data/geo_mirror/DATA/SeriesMatrix/GSE42133/GSE42133_series_matrix.txt.gz\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE63524/GSE63524_series_matrix.txt.gz ...\n", "Cache to" ] }, { "name": "stderr", "output_type": "stream", "text": [ "776.78 ms in get_probes(10)\n", " 13.49 s in load_gse( series_id platform_id..., 13274, False)\n", " 2.07 s in get_gene_fold_change(, False, 0, None)\n", "596.60 s in Load/fold for DOID_12849\n", "Meta-Analyzing DOID_12849\n", "465.19 s in meta analysis of real data for DOID_12849\n", " 1.06 s in meta analysis of permutations for DOID_12849\n", "146.15 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "466.87 s in Meta analysis for DOID_12849\n", "DONE DOID_12849 analysis\n", "1064.68 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " data/geo_mirror/DATA/SeriesMatrix/GSE63524/GSE63524_series_matrix.txt.gz\n", "18" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_13223 analysis\n", "876.80 ms in get_analysis_df(\"uterine_fibroid == 'u..., \"uterine_fibroid_contr..., '')\n", "880.97 ms in Loading dataframe for DOID_13223\n", "Matching sources: 7\n", "Excluded 1 source as single-class\n", "Stats: 6 sources, 6 series, 5 platforms, 124 samples\n", "Loading data and calculating fold change for DOID_13223\n", "Loading data for GSE2724, id = 4435\n", "396.20 ms in get_probes(2)\n", " 5.14 s in load_gse( series_id platform_id..., 4435, False)\n", " 1.69 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE28945, id = 4848\n", "113.37 ms in get_probes(929)\n", "689.04 ms in load_gse( series_id platform_id..., 4848, False)\n", "365.17 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE41386, id = 7773\n", "640.53 ms in get_probes(4)\n", " 9.32 s in load_gse( series_id platform_id..., 7773, False)\n", " 2.45 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE593, id = 10753\n", "416.41 ms in get_probes(2)\n", " 3.94 s in load_gse( series_id platform_id..., 10753, False)\n", " 1.47 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE9511, id = 11757\n", "219.17 ms in get_probes(22)\n", " 2.37 s in load_gse( series_id platform_id..., 11757, False)\n", "693.31 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE64763, id = 13408\n", "392.57 ms in get_probes(9)\n", " 14.72 s in load_gse( series_id platform_id..., 13408, False)\n", " 2.56 s in get_gene_fold_change(, False, 0, None)\n", " 47.45 s in Load/fold for DOID_13223\n", "Meta-Analyzing DOID_13223\n", "271.18 s in meta analysis of real data for DOID_13223\n", "368.96 ms in meta analysis of permutations for DOID_13223\n", "135.90 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "272.14 s in Meta analysis for DOID_13223\n", "DONE DOID_13223 analysis\n", "320.66 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:13223 uterine fibroid\n", "19" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_1324 analysis\n", " 1.58 s in get_analysis_df(\"NSCLC == 'NSCLC' or P..., \"lung_cancer_control =..., '')\n", " 1.59 s in Loading dataframe for DOID_1324\n", "Matching sources: 51\n", "Excluded 49 sources as single-class\n", "Stats: 2 sources, 2 series, 2 platforms, 800 samples\n", "Loading data and calculating fold change for DOID_1324\n", "Loading data for GSE19804, id = 2533\n", "647.04 ms in get_probes(4)\n", " 64.35 s in load_gse( series_id platform_id..., 2533, False)\n", " 4.89 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE66499, id = 13592\n", "662.28 ms in get_probes(283)\n", "245.86 s in load_gse( series_id platform_id..., 13592, False)\n", " 21.82 s in get_gene_fold_change(, False, 0, None)\n", "337.69 s in Load/fold for DOID_1324\n", "Meta-Analyzing DOID_1324\n", "310.46 s in meta analysis of real data for DOID_1324\n", "225.98 ms in meta analysis of permutations for DOID_1324\n", "149.97 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper I..., Empty DataFrame Column...)\n", "311.37 s in Meta analysis for DOID_1324\n", "DONE DOID_1324 analysis\n", "650.85 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:1324 lung cancer\n", "20" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_13241 analysis\n", "692.33 ms in get_analysis_df(\"Behcet == 'Behcet'\", \"Behcet_control == 'Be..., '')\n", "696.77 ms in Loading dataframe for DOID_13241\n", "Matching sources: 1\n", "FAIL Can't perform meta-analysis on single source\n", "836.11 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:13241 Behcet's disease\n", "21" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_13378 analysis\n", "534.16 ms in get_analysis_df(\"Kawasaki == 'Kawasaki'\", \"Kawasaki_control == '..., '')\n", "538.32 ms in Loading dataframe for DOID_13378\n", "Matching sources: 1\n", "FAIL Can't perform meta-analysis on single source\n", "670.39 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:13378 Kawasaki disease\n", "22" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_14221 analysis\n", "664.23 ms in get_analysis_df(\"MetS == 'MetS'\", \"MetS_Control == 'MetS..., '')\n", "668.46 ms in Loading dataframe for DOID_14221\n", "Matching sources: 4\n", "Excluded 4 sources as single-class\n", "FAIL Can't perform meta-analysis on no data\n", "748.79 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:14221 metabolic syndrome X\n", "23" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_14227 analysis\n", "520.80 ms in get_analysis_df(\"azoospermia == 'azoos..., \"azoospermia_control =..., '')\n", "524.97 ms in Loading dataframe for DOID_14227\n", "Matching sources: 2\n", "Stats: 2 sources, 2 series, 1 platforms, 51 samples\n", "Loading data and calculating fold change for DOID_14227\n", "Loading data for GSE45885, id = 8763\n", "418.51 ms in get_probes(283)\n", " 12.55 s in load_gse( series_id platform_id..., 8763, False)\n", " 2.25 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE45887, id = 8764\n", "416.45 ms in get_probes(283)\n", " 9.17 s in load_gse( series_id platform_id..., 8764, False)\n", " 1.89 s in get_gene_fold_change(, False, 0, None)\n", " 26.43 s in Load/fold for DOID_14227\n", "Meta-Analyzing DOID_14227\n", "345.29 s in meta analysis of real data for DOID_14227\n", "164.47 ms in meta analysis of permutations for DOID_14227\n", "137.09 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper I..., Empty DataFrame Column...)\n", "345.97 s in Meta analysis for DOID_14227\n", "DONE DOID_14227 analysis\n", "373.09 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:14227 azoospermia\n", "24" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_14330 analysis\n", "821.05 ms in get_analysis_df(\"PD == 'PD'\", \"PD_control == 'PD_con..., '')\n", "825.38 ms in Loading dataframe for DOID_14330\n", "Matching sources: 30\n", "Excluded 2 sources as single-class\n", "Excluded 1 source by min samples\n", "Stats: 27 sources, 26 series, 12 platforms, 946 samples\n", "Loading data and calculating fold change for DOID_14330\n", "Loading data for GSE18838, id = 2292\n", "550.63 ms in get_probes(280)\n", " 7.34 s in load_gse( series_id platform_id..., 2292, False)\n", " 2.70 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE19587, id = 2467\n", "393.92 ms in get_probes(9)\n", " 6.29 s in load_gse( series_id platform_id..., 2467, False)\n", "759.14 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20141, id = 2616\n", "696.28 ms in get_probes(4)\n", " 13.39 s in load_gse( series_id platform_id..., 2616, False)\n", " 3.04 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20146, id = 2619\n", "685.16 ms in get_probes(4)\n", " 12.73 s in load_gse( series_id platform_id..., 2619, False)\n", " 3.13 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20153, id = 2621\n", "626.99 ms in get_probes(4)\n", " 12.07 s in load_gse( series_id platform_id..., 2621, False)\n", " 2.83 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20163, id = 2625\n", "392.26 ms in get_probes(2)\n", " 6.31 s in load_gse( series_id platform_id..., 2625, False)\n", " 1.64 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20164, id = 2626\n", "391.40 ms in get_probes(2)\n", " 4.65 s in load_gse( series_id platform_id..., 2626, False)\n", " 1.39 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20168, id = 2628\n", "389.58 ms in get_probes(2)\n", " 7.83 s in load_gse( series_id platform_id..., 2628, False)\n", " 1.84 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20186, id = 2635\n", "404.24 ms in get_probes(2)\n", " 10.81 s in load_gse( series_id platform_id..., 2635, False)\n", " 1.95 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20291, id = 2660\n", "392.91 ms in get_probes(2)\n", " 8.94 s in load_gse( series_id platform_id..., 2660, False)\n", " 2.11 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20292, id = 2661\n", "394.65 ms in get_probes(2)\n", " 7.81 s in load_gse( series_id platform_id..., 2661, False)\n", " 1.95 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20295, id = 2663\n", "396.72 ms in get_probes(2)\n", " 21.52 s in load_gse( series_id platform_id..., 2663, False)\n", " 3.01 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20314, id = 2668\n", "391.59 ms in get_probes(2)\n", " 4.05 s in load_gse( series_id platform_id..., 2668, False)\n", " 1.33 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20333, id = 2674\n", "265.56 ms in get_probes(80)\n", " 1.85 s in load_gse( series_id platform_id..., 2674, False)\n", "802.23 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE22491, id = 3215\n", "630.85 ms in get_probes(53)\n", " 11.52 s in load_gse( series_id platform_id..., 3215, False)\n", "442.88 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE23290, id = 3414\n", "544.57 ms in get_probes(280)\n", " 4.67 s in load_gse( series_id platform_id..., 3414, False)\n", " 2.12 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE24378, id = 3706\n", "712.86 ms in get_probes(67)\n", " 16.62 s in load_gse( series_id platform_id..., 3706, False)\n", " 3.06 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE28894, id = 4829\n", "391.75 ms in get_probes(3)\n", " 26.56 s in load_gse( series_id platform_id..., 4829, False)\n", " 4.50 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE34287, id = 6132\n", " 18.10 s in get_probes(563)\n", "1064.22 s in load_gse( series_id platform_id..., 6132, False)\n", "124.06 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE34516, id = 6187\n", "549.74 ms in get_probes(280)\n", " 3.88 s in load_gse( series_id platform_id..., 6187, False)\n", " 3.69 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6613, id = 11004\n", "398.99 ms in get_probes(2)\n", " 19.66 s in load_gse( series_id platform_id..., 11004, False)\n", " 3.14 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE7621, id = 11300\n", "638.21 ms in get_probes(4)\n", " 15.20 s in load_gse( series_id platform_id..., 11300, False)\n", " 3.42 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE8397, id = 11469\n", "391.71 ms in get_probes(2)\n", "344.13 ms in get_probes(50)\n", " 26.22 s in load_gse( series_id platform_id..., 11469, False)\n", " 4.15 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE43490, id = 12100\n", "506.59 ms in get_probes(53)\n", " 10.85 s in load_gse( series_id platform_id..., 12100, False)\n", " 2.85 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54282, id = 12418\n", "384.50 ms in get_probes(1367)\n", " 4.69 s in load_gse( series_id platform_id..., 12418, False)\n", " 1.29 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE57475, id = 12634\n", "496.94 ms in get_probes(389)\n", " 64.82 s in load_gse( series_id platform_id..., 12634, False)\n", " 7.32 s in get_gene_fold_change(, False, 0, None)\n", "1596.87 s in Load/fold for DOID_14330\n", "Meta-Analyzing DOID_14330\n", "469.09 s in meta analysis of real data for DOID_14330\n", " 6.42 s in meta analysis of permutations for DOID_14330\n", "146.15 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "476.15 s in Meta analysis for DOID_14330\n", "DONE DOID_14330 analysis\n", "2074.15 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:14330 Parkinson's disease\n", "25" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_1595 analysis\n", " 2.30 s in get_analysis_df(\"Depression == 'Depres..., \"MDD_control == 'MDD_c..., '')\n", " 2.30 s in Loading dataframe for DOID_1595\n", "Matching sources: 19\n", "Excluded 5 sources as single-class\n", "Stats: 14 sources, 14 series, 6 platforms, 533 samples\n", "Loading data and calculating fold change for DOID_1595\n", "Loading data for GSE12654, id = 704\n", "301.68 ms in get_probes(7)\n", " 8.12 s in load_gse( series_id platform_id..., 704, False)\n", " 1.20 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE19738, id = 2518\n", "729.91 ms in get_probes(282)\n", " 40.29 s in load_gse( series_id platform_id..., 2518, False)\n", " 7.71 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE39653, id = 7363\n", "770.22 ms in get_probes(674)\n", " 28.74 s in load_gse( series_id platform_id..., 7363, False)\n", " 3.49 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54562, id = 10202\n", "493.64 ms in get_probes(389)\n", " 14.14 s in load_gse( series_id platform_id..., 10202, False)\n", " 1.75 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54563, id = 10203\n", "504.69 ms in get_probes(389)\n", " 31.29 s in load_gse( series_id platform_id..., 10203, False)\n", " 3.42 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54564, id = 10204\n", "508.15 ms in get_probes(389)\n", " 24.86 s in load_gse( series_id platform_id..., 10204, False)\n", " 2.92 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54565, id = 10205\n", "633.66 ms in get_probes(4)\n", " 27.51 s in load_gse( series_id platform_id..., 10205, False)\n", " 3.53 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54566, id = 10206\n", "637.70 ms in get_probes(4)\n", " 24.99 s in load_gse( series_id platform_id..., 10206, False)\n", " 3.33 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54567, id = 10207\n", "629.40 ms in get_probes(4)\n", " 20.99 s in load_gse( series_id platform_id..., 10207, False)\n", " 3.54 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54568, id = 10208\n", "627.24 ms in get_probes(4)\n", " 21.87 s in load_gse( series_id platform_id..., 10208, False)\n", " 3.72 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54570, id = 10210\n", "394.17 ms in get_probes(2)\n", " 6.07 s in load_gse( series_id platform_id..., 10210, False)\n", " 1.89 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54571, id = 10211\n", "628.97 ms in get_probes(4)\n", " 20.05 s in load_gse( series_id platform_id..., 10211, False)\n", " 3.47 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54572, id = 10212\n", "625.43 ms in get_probes(4)\n", " 18.49 s in load_gse( series_id platform_id..., 10212, False)\n", " 3.26 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54575, id = 10213\n", "393.65 ms in get_probes(2)\n", " 5.83 s in load_gse( series_id platform_id..., 10213, False)\n", " 1.75 s in get_gene_fold_change(, False, 0, None)\n", "344.13 s in Load/fold for DOID_1595\n", "Meta-Analyzing DOID_1595\n", "450.85 s in meta analysis of real data for DOID_1595\n", " 1.59 s in meta analysis of permutations for DOID_1595\n", "133.99 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "453.05 s in Meta analysis for DOID_1595\n", "DONE DOID_1595 analysis\n", "799.72 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:1595 endogenous depression\n", "26" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_1612 analysis\n", " 1.78 s in get_analysis_df(\"breast_cancer == 'bre..., \"breast_cancer_control..., '')\n", " 1.78 s in Loading dataframe for DOID_1612\n", "Matching sources: 63\n", "Excluded 33 sources as single-class\n", "Excluded 1 source by min samples\n", "Stats: 29 sources, 25 series, 16 platforms, 1819 samples\n", "Loading data and calculating fold change for DOID_1612\n", "Loading data for GSE10780, id = 206\n", "643.49 ms in get_probes(4)\n", "118.98 s in load_gse( series_id platform_id..., 206, False)\n", " 13.50 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE10797, id = 212\n", "397.68 ms in get_probes(9)\n", " 21.71 s in load_gse( series_id platform_id..., 212, False)\n", " 2.98 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE10810, id = 218\n", "643.77 ms in get_probes(4)\n", " 16.22 s in load_gse( series_id platform_id..., 218, False)\n", " 4.79 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE10885, id = 238\n", "370.63 ms in get_probes(83)\n", "370.30 ms in get_probes(49)\n", " 40.35 s in load_gse( series_id platform_id..., 238, False)\n", " 6.74 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE10886, id = 239\n", "378.77 ms in get_probes(83)\n", " 36.45 s in load_gse( series_id platform_id..., 239, False)\n", " 3.98 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE11545, id = 412\n", "365.76 ms in get_probes(60)\n", " 25.41 s in load_gse( series_id platform_id..., 412, False)\n", " 1.84 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE13293, id = 864\n", "115.03 ms in get_probes(399)\n", "118.23 ms in get_probes(401)\n", " 22.48 s in load_gse( series_id platform_id..., 864, False)\n", "872.85 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE14548, id = 1177\n", "704.84 ms in get_probes(67)\n", " 50.12 s in load_gse( series_id platform_id..., 1177, False)\n", " 6.45 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE15852, id = 1538\n", "394.83 ms in get_probes(2)\n", " 18.36 s in load_gse( series_id platform_id..., 1538, False)\n", " 3.63 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20266, id = 2653\n", "625.49 ms in get_probes(4)\n", " 12.33 s in load_gse( series_id platform_id..., 2653, False)\n", " 3.01 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20437, id = 2693\n", "393.14 ms in get_probes(2)\n", " 8.86 s in load_gse( series_id platform_id..., 2693, False)\n", " 2.32 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE21947, id = 3053\n", "391.14 ms in get_probes(2)\n", " 6.94 s in load_gse( series_id platform_id..., 3053, False)\n", " 1.60 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE22384, id = 3185\n", " 1.94 s in get_probes(517)\n", " 1.56 s in get_probes(519)\n", " 2.03 s in get_probes(520)\n", "284.82 s in load_gse( series_id platform_id..., 3185, False)\n", " 39.56 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE26910, id = 4354\n", "634.81 ms in get_probes(4)\n", " 15.90 s in load_gse( series_id platform_id..., 4354, False)\n", " 2.57 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27120, id = 4400\n", "630.03 ms in get_probes(4)\n", " 52.33 s in load_gse( series_id platform_id..., 4400, False)\n", " 3.75 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29044, id = 4880\n", "627.92 ms in get_probes(4)\n", " 63.95 s in load_gse( series_id platform_id..., 4880, False)\n", " 8.85 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29431, id = 4975\n", "627.35 ms in get_probes(4)\n", " 32.62 s in load_gse( series_id platform_id..., 4975, False)\n", " 5.90 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE32641, id = 5764\n", "368.45 ms in get_probes(49)\n", " 26.35 s in load_gse( series_id platform_id..., 5764, False)\n", " 3.91 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE33447, id = 5940\n", "704.63 ms in get_probes(1010)\n", " 9.58 s in load_gse( series_id platform_id..., 5940, False)\n", " 2.20 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE36295, id = 6622\n", "414.92 ms in get_probes(283)\n", " 17.57 s in load_gse( series_id platform_id..., 6622, False)\n", " 2.35 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE38959, id = 7206\n", "708.55 ms in get_probes(10)\n", " 22.11 s in load_gse( series_id platform_id..., 7206, False)\n", " 3.49 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE42568, id = 8064\n", "626.59 ms in get_probes(4)\n", " 70.99 s in load_gse( series_id platform_id..., 8064, False)\n", " 8.84 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE50567, id = 9572\n", "644.37 ms in get_probes(4)\n", " 27.73 s in load_gse( series_id platform_id..., 9572, False)\n", " 3.64 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE57297, id = 10562\n", "543.38 ms in get_probes(1339)\n", " 20.45 s in load_gse( series_id platform_id..., 10562, False)\n", " 3.09 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6130, id = 10873\n", "364.99 ms in get_probes(49)\n", " 10.84 s in load_gse( series_id platform_id..., 10873, False)\n", " 2.31 s in get_gene_fold_change(, False, 0, None)\n", "1187.38 s in Load/fold for DOID_1612\n", "Meta-Analyzing DOID_1612\n", "492.34 s in meta analysis of real data for DOID_1612\n", " 3.72 s in meta analysis of permutations for DOID_1612\n", "134.94 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "496.68 s in Meta analysis for DOID_1612\n", "DONE DOID_1612 analysis\n", "1686.18 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:1612 breast cancer\n", "27" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_1686 analysis\n", " 1.70 s in get_analysis_df(\"glaucoma == 'glaucoma'\", \"glaucoma_control == '..., '')\n", " 1.70 s in Loading dataframe for DOID_1686\n", "Matching sources: 11\n", "Excluded 1 source as single-class\n", "Excluded 3 sources by min samples\n", "Stats: 7 sources, 6 series, 5 platforms, 138 samples\n", "Loading data and calculating fold change for DOID_1686\n", "Loading data for GSE2378, id = 3554\n", "309.04 ms in get_probes(7)\n", " 3.09 s in load_gse( series_id platform_id..., 3554, False)\n", "748.82 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27276, id = 4448\n", "404.38 ms in get_probes(39)\n", " 22.35 s in load_gse( series_id platform_id..., 4448, False)\n", " 2.07 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE45570, id = 8697\n", "544.98 ms in get_probes(280)\n", " 5.84 s in load_gse( series_id platform_id..., 8697, False)\n", " 2.06 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE9944, id = 11879\n", "394.91 ms in get_probes(9)\n", "472.41 ms in get_probes(7)\n", " 12.78 s in load_gse( series_id platform_id..., 11879, False)\n", " 3.18 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27057, id = 11946\n", " 38.89 ms in get_probes(1703)\n", "977.82 ms in load_gse( series_id platform_id..., 11946, False)\n", "192.35 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27058, id = 11947\n", " 39.14 ms in get_probes(1703)\n", "899.34 ms in load_gse( series_id platform_id..., 11947, False)\n", "175.76 ms in get_gene_fold_change(, False, 0, None)\n", " 56.01 s in Load/fold for DOID_1686\n", "Meta-Analyzing DOID_1686\n", "336.07 s in meta analysis of real data for DOID_1686\n", "319.10 ms in meta analysis of permutations for DOID_1686\n", "135.90 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "336.99 s in Meta analysis for DOID_1686\n", "DONE DOID_1686 analysis\n", "394.90 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:1686 glaucoma\n", "28" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_1793 analysis\n", "893.86 ms in get_analysis_df(\"pancreatic_cancer == ..., \"pancreatic_cancer_con..., '')\n", "898.07 ms in Loading dataframe for DOID_1793\n", "Matching sources: 28\n", "Excluded 16 sources as single-class\n", "Excluded 3 sources by min samples\n", "Stats: 9 sources, 9 series, 5 platforms, 250 samples\n", "Loading data and calculating fold change for DOID_1793\n", "Loading data for GSE14245, id = 1080\n", "637.77 ms in get_probes(4)\n", " 13.65 s in load_gse( series_id platform_id..., 1080, False)\n", " 2.49 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE15932, id = 1550\n", "640.27 ms in get_probes(4)\n", " 20.37 s in load_gse( series_id platform_id..., 1550, False)\n", " 3.43 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE19279, id = 2400\n", "404.20 ms in get_probes(2)\n", " 5.50 s in load_gse( series_id platform_id..., 2400, False)\n", " 1.15 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE19650, id = 2485\n", "647.77 ms in get_probes(4)\n", " 14.47 s in load_gse( series_id platform_id..., 2485, False)\n", " 3.32 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE21163, id = 2867\n", " 4.63 s in get_probes(54)\n", " 70.25 s in load_gse( series_id platform_id..., 2867, False)\n", " 24.09 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE22780, id = 3283\n", "626.75 ms in get_probes(4)\n", " 12.48 s in load_gse( series_id platform_id..., 3283, False)\n", " 2.87 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE23397, id = 3450\n", " 4.69 s in get_probes(54)\n", " 84.41 s in load_gse( series_id platform_id..., 3450, False)\n", " 24.03 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE28735, id = 4791\n", "445.42 ms in get_probes(283)\n", " 25.83 s in load_gse( series_id platform_id..., 4791, False)\n", " 4.24 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE30134, id = 5154\n", "149.89 ms in get_probes(963)\n", " 1.56 s in load_gse( series_id platform_id..., 5154, False)\n", "433.51 ms in get_gene_fold_change(, False, 0, None)\n", "320.62 s in Load/fold for DOID_1793\n", "Meta-Analyzing DOID_1793\n", "440.56 s in meta analysis of real data for DOID_1793\n", " 3.26 s in meta analysis of permutations for DOID_1793\n", "137.09 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "444.43 s in Meta analysis for DOID_1793\n", "DONE DOID_1793 analysis\n", "766.17 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:1793 pancreatic cancer\n", "29" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_1909 analysis\n", " 1.87 s in get_analysis_df(\"melanoma == 'melanoma'\", \"melanoma_control == '..., '')\n", " 1.87 s in Loading dataframe for DOID_1909\n", "Matching sources: 48\n", "Excluded 35 sources as single-class\n", "Excluded 1 source by min samples\n", "Stats: 12 sources, 9 series, 5 platforms, 487 samples\n", "Loading data and calculating fold change for DOID_1909\n", "Loading data for GSE11907, id = 488\n", "401.26 ms in get_probes(2)\n", "350.03 ms in get_probes(50)\n", "101.16 s in load_gse( series_id platform_id..., 488, False)\n", " 4.24 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE15605, id = 1479\n", "843.89 ms in get_probes(4)\n", " 40.85 s in load_gse( series_id platform_id..., 1479, False)\n", " 3.87 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE3189, id = 5563\n", "400.24 ms in get_probes(2)\n", " 13.98 s in load_gse( series_id platform_id..., 5563, False)\n", " 2.74 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE44660, id = 8515\n", "545.60 ms in get_probes(280)\n", " 6.38 s in load_gse( series_id platform_id..., 8515, False)\n", " 2.51 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE46517, id = 8884\n", "397.11 ms in get_probes(2)\n", " 32.56 s in load_gse( series_id platform_id..., 8884, False)\n", " 4.01 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE4840, id = 9237\n", "415.91 ms in get_probes(2)\n", "426.68 ms in get_probes(50)\n", " 9.22 s in load_gse( series_id platform_id..., 9237, False)\n", " 2.54 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE4845, id = 9251\n", "393.28 ms in get_probes(2)\n", "436.85 ms in get_probes(50)\n", " 15.27 s in load_gse( series_id platform_id..., 9251, False)\n", " 3.12 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE7469, id = 11250\n", "712.27 ms in get_probes(26)\n", " 12.43 s in load_gse( series_id platform_id..., 11250, False)\n", " 2.49 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE7553, id = 11277\n", "622.82 ms in get_probes(4)\n", " 48.66 s in load_gse( series_id platform_id..., 11277, False)\n", " 5.80 s in get_gene_fold_change(, False, 0, None)\n", "314.85 s in Load/fold for DOID_1909\n", "Meta-Analyzing DOID_1909\n", "417.25 s in meta analysis of real data for DOID_1909\n", " 1.05 s in meta analysis of permutations for DOID_1909\n", "134.94 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "418.92 s in Meta analysis for DOID_1909\n", "DONE DOID_1909 analysis\n", "735.87 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:1909 melanoma\n", "30" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_1936 analysis\n", " 1.12 s in get_analysis_df(\"atherosclerosis == 'a..., \"atherosclerosis_contr..., '')\n", " 1.13 s in Loading dataframe for DOID_1936\n", "Matching sources: 6\n", "Excluded 1 source as single-class\n", "Excluded 1 source by min samples\n", "Stats: 4 sources, 4 series, 4 platforms, 346 samples\n", "Loading data and calculating fold change for DOID_1936\n", "Loading data for GSE20129, id = 2612\n", "385.46 ms in get_probes(3)\n", " 30.05 s in load_gse( series_id platform_id..., 2612, False)\n", " 4.61 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE23746, id = 3545\n", "375.64 ms in get_probes(74)\n", " 15.65 s in load_gse( series_id platform_id..., 3545, False)\n", " 2.66 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE37356, id = 6873\n", "517.42 ms in get_probes(674)\n", " 29.25 s in load_gse( series_id platform_id..., 6873, False)\n", " 4.64 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE9874, id = 11861\n", "389.88 ms in get_probes(2)\n", " 13.91 s in load_gse( series_id platform_id..., 11861, False)\n", " 2.91 s in get_gene_fold_change(, False, 0, None)\n", "104.86 s in Load/fold for DOID_1936\n", "Meta-Analyzing DOID_1936\n", "367.74 s in meta analysis of real data for DOID_1936\n", "306.02 ms in meta analysis of permutations for DOID_1936\n", "136.14 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "368.65 s in Meta analysis for DOID_1936\n", "DONE DOID_1936 analysis\n", "474.82 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:1936 atherosclerosis\n", "31" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_219 analysis\n", "791.29 ms in get_analysis_df(\"colon_cancer == 'colo..., \"colon_cancer_control ..., '')\n", "795.60 ms in Loading dataframe for DOID_219\n", "Matching sources: 5\n", "Excluded 1 source as single-class\n", "Stats: 4 sources, 3 series, 4 platforms, 275 samples\n", "Loading data and calculating fold change for DOID_219\n", "Loading data for GSE36400, id = 6646\n", "542.89 ms in get_probes(280)\n", " 5.46 s in load_gse( series_id platform_id..., 6646, False)\n", " 1.56 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE7466, id = 11249\n", " 75.17 ms in get_probes(821)\n", " 74.89 ms in get_probes(823)\n", " 13.50 s in load_gse( series_id platform_id..., 11249, False)\n", "552.06 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE68468, id = 13736\n", "390.12 ms in get_probes(2)\n", " 83.88 s in load_gse( series_id platform_id..., 13736, False)\n", " 8.33 s in get_gene_fold_change(, False, 0, None)\n", "114.04 s in Load/fold for DOID_219\n", "Meta-Analyzing DOID_219\n", "220.42 s in meta analysis of real data for DOID_219\n", "191.45 ms in meta analysis of permutations for DOID_219\n", "135.90 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper I..., Empty DataFrame Column...)\n", "221.19 s in Meta analysis for DOID_219\n", "DONE DOID_219 analysis\n", "336.20 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:219 colon cancer\n", "32" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_2377 analysis\n", "960.37 ms in get_analysis_df(\"MS == 'MS'\", \"MS_control == 'MS_con..., '')\n", "964.60 ms in Loading dataframe for DOID_2377\n", "Matching sources: 27\n", "Excluded 3 sources as single-class\n", "Excluded 2 sources by min samples\n", "Stats: 22 sources, 21 series, 9 platforms, 1781 samples\n", "Loading data and calculating fold change for DOID_2377\n", "Loading data for GSE10064, id = 17\n", "412.18 ms in get_probes(12)\n", " 10.82 s in load_gse( series_id platform_id..., 17, False)\n", " 1.67 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE13732, id = 973\n", "633.60 ms in get_probes(4)\n", " 73.07 s in load_gse( series_id platform_id..., 973, False)\n", " 8.85 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE14895, id = 1280\n", "388.18 ms in get_probes(9)\n", "394.69 ms in get_probes(2)\n", " 15.78 s in load_gse( series_id platform_id..., 1280, False)\n", " 3.24 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE16461, id = 1688\n", "633.89 ms in get_probes(4)\n", " 12.62 s in load_gse( series_id platform_id..., 1688, False)\n", " 2.80 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17048, id = 1837\n", "686.11 ms in get_probes(389)\n", " 56.78 s in load_gse( series_id platform_id..., 1837, False)\n", " 6.34 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17393, id = 1917\n", "387.54 ms in get_probes(9)\n", " 5.45 s in load_gse( series_id platform_id..., 1917, False)\n", " 1.57 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17449, id = 1929\n", "387.68 ms in get_probes(9)\n", " 8.37 s in load_gse( series_id platform_id..., 1929, False)\n", " 1.87 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE21942, id = 3050\n", "623.83 ms in get_probes(4)\n", " 15.67 s in load_gse( series_id platform_id..., 3050, False)\n", " 3.52 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE23832, id = 3564\n", "408.93 ms in get_probes(283)\n", " 4.66 s in load_gse( series_id platform_id..., 3564, False)\n", " 1.59 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE26484, id = 4227\n", "620.18 ms in get_probes(4)\n", " 9.96 s in load_gse( series_id platform_id..., 4227, False)\n", " 2.50 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27688, id = 4537\n", "638.91 ms in get_probes(53)\n", " 12.57 s in load_gse( series_id platform_id..., 4537, False)\n", " 2.75 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE32645, id = 5766\n", "682.50 ms in get_probes(10)\n", " 10.10 s in load_gse( series_id platform_id..., 5766, False)\n", " 1.82 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE32915, id = 5810\n", "652.66 ms in get_probes(10)\n", " 11.46 s in load_gse( series_id platform_id..., 5810, False)\n", " 2.09 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE32988, id = 5831\n", "659.84 ms in get_probes(53)\n", " 24.66 s in load_gse( series_id platform_id..., 5831, False)\n", " 3.46 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE41848, id = 7884\n", " 39.78 ms in get_probes(1289)\n", " 44.96 s in load_gse( series_id platform_id..., 7884, False)\n", "307.71 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE41849, id = 7885\n", " 39.34 ms in get_probes(1289)\n", " 20.77 s in load_gse( series_id platform_id..., 7885, False)\n", "231.72 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE41850, id = 7887\n", " 39.17 ms in get_probes(1289)\n", "160.56 s in load_gse( series_id platform_id..., 7887, False)\n", "400.87 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE41890, id = 7897\n", "414.89 ms in get_probes(283)\n", " 24.10 s in load_gse( series_id platform_id..., 7897, False)\n", " 3.31 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE43591, id = 8314\n", "619.29 ms in get_probes(4)\n", " 15.75 s in load_gse( series_id platform_id..., 8314, False)\n", " 3.02 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE37750, id = 12030\n", "619.96 ms in get_probes(4)\n", " 18.00 s in load_gse( series_id platform_id..., 12030, False)\n", " 3.28 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE59085, id = 12788\n", "620.90 ms in get_probes(4)\n", " 16.50 s in load_gse( series_id platform_id..., 12788, False)\n", " 3.22 s in get_gene_fold_change(, False, 0, None)\n", "637.76 s in Load/fold for DOID_2377\n", "Meta-Analyzing DOID_2377\n", "471.19 s in meta analysis of real data for DOID_2377\n", " 1.95 s in meta analysis of permutations for DOID_2377\n", "129.94 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "473.76 s in Meta analysis for DOID_2377\n", "DONE DOID_2377 analysis\n", "1112.79 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:2377 multiple sclerosis\n", "33" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_2394 analysis\n", " 1.07 s in get_analysis_df(\"ovarian_cancer == 'ov..., \"ovarian_cancer_contro..., '')\n", " 1.08 s in Loading dataframe for DOID_2394\n", "Matching sources: 4\n", "Excluded 1 source as single-class\n", "Stats: 3 sources, 3 series, 2 platforms, 123 samples\n", "Loading data and calculating fold change for DOID_2394\n", "Loading data for GSE29220, id = 4918\n", "634.25 ms in get_probes(4)\n", " 16.86 s in load_gse( series_id platform_id..., 4918, False)\n", " 3.24 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE31682, id = 5516\n", "350.25 ms in get_probes(60)\n", " 18.72 s in load_gse( series_id platform_id..., 5516, False)\n", " 2.62 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE38666, id = 7137\n", "624.42 ms in get_probes(4)\n", " 25.57 s in load_gse( series_id platform_id..., 7137, False)\n", " 3.87 s in get_gene_fold_change(, False, 0, None)\n", " 72.05 s in Load/fold for DOID_2394\n", "Meta-Analyzing DOID_2394\n", "393.79 s in meta analysis of real data for DOID_2394\n", "335.69 ms in meta analysis of permutations for DOID_2394\n", "128.03 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "394.72 s in Meta analysis for DOID_2394\n", "DONE DOID_2394 analysis\n", "468.02 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:2394 ovarian cancer\n", "34" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_2531 analysis\n", " 1.64 s in get_analysis_df(\"AML_Tissue == 'AML_Ti..., \"AML_Control == 'AML_C..., '')\n", " 1.64 s in Loading dataframe for DOID_2531\n", "Matching sources: 95\n", "Excluded 82 sources as single-class\n", "Stats: 13 sources, 13 series, 5 platforms, 755 samples\n", "Loading data and calculating fold change for DOID_2531\n", "Loading data for GSE10746, id = 198\n", "636.98 ms in get_probes(4)\n", " 9.82 s in load_gse( series_id platform_id..., 198, False)\n", " 2.61 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE13591, id = 938\n", "401.84 ms in get_probes(2)\n", " 40.19 s in load_gse( series_id platform_id..., 938, False)\n", " 4.67 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17054, id = 1838\n", "639.44 ms in get_probes(4)\n", " 14.18 s in load_gse( series_id platform_id..., 1838, False)\n", " 2.69 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE24870, id = 3848\n", "408.95 ms in get_probes(9)\n", " 10.12 s in load_gse( series_id platform_id..., 3848, False)\n", " 2.44 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27838, id = 4550\n", "626.86 ms in get_probes(4)\n", " 17.50 s in load_gse( series_id platform_id..., 4550, False)\n", " 3.77 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE36474, id = 6658\n", "623.81 ms in get_probes(4)\n", " 8.55 s in load_gse( series_id platform_id..., 6658, False)\n", " 1.84 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE39754, id = 7392\n", "544.41 ms in get_probes(280)\n", " 38.87 s in load_gse( series_id platform_id..., 7392, False)\n", " 9.43 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE43176, id = 8218\n", "411.94 ms in get_probes(2)\n", " 20.50 s in load_gse( series_id platform_id..., 8218, False)\n", " 3.06 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5900, id = 10734\n", "643.24 ms in get_probes(4)\n", " 41.88 s in load_gse( series_id platform_id..., 10734, False)\n", " 4.05 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6477, id = 10950\n", "402.80 ms in get_probes(2)\n", " 30.19 s in load_gse( series_id platform_id..., 10950, False)\n", " 5.53 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6691, id = 11013\n", "392.90 ms in get_probes(2)\n", " 13.11 s in load_gse( series_id platform_id..., 11013, False)\n", " 1.60 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE7116, id = 11154\n", "626.38 ms in get_probes(4)\n", " 16.30 s in load_gse( series_id platform_id..., 11154, False)\n", " 3.44 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE983, id = 11844\n", "218.45 ms in get_probes(22)\n", " 1.87 s in load_gse( series_id platform_id..., 11844, False)\n", "663.65 ms in get_gene_fold_change(, False, 0, None)\n", "314.45 s in Load/fold for DOID_2531\n", "Meta-Analyzing DOID_2531\n", "405.78 s in meta analysis of real data for DOID_2531\n", " 1.33 s in meta analysis of permutations for DOID_2531\n", "133.99 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "407.71 s in Meta analysis for DOID_2531\n", "DONE DOID_2531 analysis\n", "724.11 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:2531 hematologic cancer\n", "35" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_263 analysis\n", " 1.22 s in get_analysis_df(\"RCC == 'RCC'\", \"RCC_Control == 'RCC_C..., '')\n", " 1.22 s in Loading dataframe for DOID_263\n", "Matching sources: 60\n", "Excluded 37 sources as single-class\n", "Excluded 2 sources by min samples\n", "Stats: 21 sources, 17 series, 13 platforms, 1536 samples\n", "Loading data and calculating fold change for DOID_263\n", "Loading data for GSE12606, id = 685\n", "625.26 ms in get_probes(4)\n", " 9.55 s in load_gse( series_id platform_id..., 685, False)\n", " 2.57 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE14762, id = 1230\n", " 40.30 ms in get_probes(471)\n", " 4.45 s in load_gse( series_id platform_id..., 1230, False)\n", "320.08 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE15641, id = 1490\n", "391.32 ms in get_probes(2)\n", " 18.86 s in load_gse( series_id platform_id..., 1490, False)\n", " 3.17 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17816, id = 2030\n", "333.72 ms in get_probes(588)\n", " 10.10 s in load_gse( series_id platform_id..., 2030, False)\n", " 2.02 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17818, id = 2031\n", "347.50 ms in get_probes(588)\n", " 24.94 s in load_gse( series_id platform_id..., 2031, False)\n", " 3.47 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17895, id = 2051\n", "344.39 ms in get_probes(588)\n", " 32.86 s in load_gse( series_id platform_id..., 2051, False)\n", " 4.56 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE26574, id = 4253\n", "364.97 ms in get_probes(875)\n", " 18.31 s in load_gse( series_id platform_id..., 4253, False)\n", " 1.54 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE3, id = 5117\n", "602.69 ms in get_probes(258)\n", "570.71 ms in get_probes(259)\n", "209.46 s in load_gse( series_id platform_id..., 5117, False)\n", " 12.90 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE36895, id = 6744\n", "637.64 ms in get_probes(4)\n", " 51.41 s in load_gse( series_id platform_id..., 6744, False)\n", " 5.08 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE40435, id = 7557\n", "534.00 ms in get_probes(674)\n", "109.20 s in load_gse( series_id platform_id..., 7557, False)\n", " 9.90 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE46699, id = 8919\n", "627.50 ms in get_probes(4)\n", " 81.27 s in load_gse( series_id platform_id..., 8919, False)\n", " 10.05 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE47032, id = 8982\n", "541.08 ms in get_probes(280)\n", " 4.84 s in get_probes(54)\n", " 70.78 s in load_gse( series_id platform_id..., 8982, False)\n", " 25.03 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE53000, id = 9972\n", "424.36 ms in get_probes(283)\n", " 26.09 s in load_gse( series_id platform_id..., 9972, False)\n", " 3.17 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE53757, id = 10076\n", "634.42 ms in get_probes(4)\n", " 81.12 s in load_gse( series_id platform_id..., 10076, False)\n", " 11.13 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6344, id = 10912\n", "392.80 ms in get_probes(2)\n", "334.30 ms in get_probes(50)\n", " 11.07 s in load_gse( series_id platform_id..., 10912, False)\n", " 2.79 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE7367, id = 11222\n", "154.50 ms in get_probes(963)\n", " 2.98 s in load_gse( series_id platform_id..., 11222, False)\n", "575.03 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE781, id = 11344\n", "417.10 ms in get_probes(2)\n", "352.93 ms in get_probes(50)\n", " 10.61 s in load_gse( series_id platform_id..., 11344, False)\n", " 2.31 s in get_gene_fold_change(, False, 0, None)\n", "881.23 s in Load/fold for DOID_263\n", "Meta-Analyzing DOID_263\n", "456.84 s in meta analysis of real data for DOID_263\n", " 2.83 s in meta analysis of permutations for DOID_263\n", "140.19 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "460.28 s in Meta analysis for DOID_263\n", "DONE DOID_263 analysis\n", "1343.04 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:263 kidney cancer\n", "36" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_2841 analysis\n", " 1.49 s in get_analysis_df(\"asthma == 'asthma'\", \"asthma_control == 'as..., '')\n", " 1.50 s in Loading dataframe for DOID_2841\n", "Matching sources: 14\n", "Stats: 14 sources, 13 series, 9 platforms, 1486 samples\n", "Loading data and calculating fold change for DOID_2841\n", "Loading data for GSE19187, id = 2377\n", "416.18 ms in get_probes(283)\n", " 14.56 s in load_gse( series_id platform_id..., 2377, False)\n", " 2.04 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27011, id = 4384\n", "438.88 ms in get_probes(283)\n", " 22.72 s in load_gse( series_id platform_id..., 4384, False)\n", " 2.95 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27876, id = 4561\n", "693.51 ms in get_probes(53)\n", " 10.67 s in load_gse( series_id platform_id..., 4561, False)\n", " 2.19 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE4302, id = 8180\n", "628.39 ms in get_probes(4)\n", " 75.85 s in load_gse( series_id platform_id..., 8180, False)\n", " 8.29 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE44037, id = 8399\n", "897.74 ms in get_probes(901)\n", " 20.98 s in load_gse( series_id platform_id..., 8399, False)\n", " 3.21 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE46171, id = 8818\n", "725.52 ms in get_probes(1363)\n", "688.35 ms in get_probes(53)\n", " 42.90 s in load_gse( series_id platform_id..., 8818, False)\n", " 6.18 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5272, id = 9938\n", "735.95 ms in get_probes(26)\n", "129.40 s in load_gse( series_id platform_id..., 9938, False)\n", " 9.59 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54605, id = 10215\n", " 42.46 ms in get_probes(1454)\n", "337.32 ms in load_gse( series_id platform_id..., 10215, False)\n", "327.41 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE56396, id = 10453\n", "412.76 ms in get_probes(283)\n", " 29.16 s in load_gse( series_id platform_id..., 10453, False)\n", " 4.82 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE8052, id = 11413\n", "642.58 ms in get_probes(4)\n", "180.37 s in load_gse( series_id platform_id..., 11413, False)\n", " 27.32 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE8190, id = 11437\n", "768.50 ms in get_probes(26)\n", "135.63 s in load_gse( series_id platform_id..., 11437, False)\n", " 8.79 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE40732, id = 12071\n", "773.59 ms in get_probes(1269)\n", " 80.98 s in load_gse( series_id platform_id..., 12071, False)\n", " 12.38 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE67472, id = 13661\n", " 39.90 ms in get_probes(1369)\n", " 22.81 s in load_gse( series_id platform_id..., 13661, False)\n", "310.30 ms in get_gene_fold_change(, False, 0, None)\n", "859.46 s in Load/fold for DOID_2841\n", "Meta-Analyzing DOID_2841\n", "467.77 s in meta analysis of real data for DOID_2841\n", " 1.24 s in meta analysis of permutations for DOID_2841\n", "134.94 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "469.63 s in Meta analysis for DOID_2841\n", "DONE DOID_2841 analysis\n", "1330.83 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:2841 asthma\n", "37" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_2986 analysis\n", " 1.06 s in get_analysis_df(\"IgA_nephropathy == 'I..., \"IgA_nephropathy_contr..., '')\n", " 1.06 s in Loading dataframe for DOID_2986\n", "Matching sources: 6\n", "Stats: 6 sources, 5 series, 3 platforms, 161 samples\n", "Loading data and calculating fold change for DOID_2986\n", "Loading data for GSE14795, id = 1241\n", "400.31 ms in get_probes(2)\n", " 6.06 s in load_gse( series_id platform_id..., 1241, False)\n", " 1.70 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE35487, id = 6431\n", "391.72 ms in get_probes(2)\n", " 9.15 s in load_gse( series_id platform_id..., 6431, False)\n", " 1.97 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE35488, id = 6432\n", "284.37 ms in get_probes(1019)\n", " 5.52 s in load_gse( series_id platform_id..., 6432, False)\n", " 1.27 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE35489, id = 6433\n", "294.34 ms in get_probes(1019)\n", "575.04 ms in get_probes(2)\n", " 14.90 s in load_gse( series_id platform_id..., 6433, False)\n", " 2.08 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE58539, id = 12726\n", "530.63 ms in get_probes(674)\n", " 12.73 s in load_gse( series_id platform_id..., 12726, False)\n", " 2.36 s in get_gene_fold_change(, False, 0, None)\n", " 59.49 s in Load/fold for DOID_2986\n", "Meta-Analyzing DOID_2986\n", "272.07 s in meta analysis of real data for DOID_2986\n", "367.14 ms in meta analysis of permutations for DOID_2986\n", "135.18 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "273.03 s in Meta analysis for DOID_2986\n", "DONE DOID_2986 analysis\n", "333.76 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:2986 IgA glomerulonephritis\n", "38" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_2998 analysis\n", "860.02 ms in get_analysis_df(\"testicular_cancer == ..., \"testicular_cancer_con..., '')\n", "864.55 ms in Loading dataframe for DOID_2998\n", "Matching sources: 0\n", "FAIL Can't perform meta-analysis on no data\n", "929.62 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:2998 testicular cancer\n", "39" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_3083 analysis\n", "882.74 ms in get_analysis_df(\"COPD == 'COPD'\", \"COPD_control == 'COPD..., '')\n", "887.22 ms in Loading dataframe for DOID_3083\n", "Matching sources: 22\n", "Excluded 4 sources as single-class\n", "Stats: 18 sources, 17 series, 7 platforms, 1720 samples\n", "Loading data and calculating fold change for DOID_3083\n", "Loading data for GSE10006, id = 4\n", "629.08 ms in get_probes(4)\n", " 48.65 s in load_gse( series_id platform_id..., 4, False)\n", " 7.68 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE11784, id = 450\n", "630.11 ms in get_probes(4)\n", " 86.30 s in load_gse( series_id platform_id..., 450, False)\n", " 11.75 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE12472, id = 652\n", "487.48 ms in get_probes(26)\n", " 9.32 s in load_gse( series_id platform_id..., 652, False)\n", " 3.72 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE16972, id = 1810\n", "415.70 ms in get_probes(2)\n", " 4.47 s in load_gse( series_id platform_id..., 1810, False)\n", " 1.48 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE19407, id = 2430\n", "640.41 ms in get_probes(4)\n", " 70.22 s in load_gse( series_id platform_id..., 2430, False)\n", " 10.60 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20257, id = 2650\n", "632.61 ms in get_probes(4)\n", " 73.93 s in load_gse( series_id platform_id..., 2650, False)\n", " 10.54 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27536, id = 4511\n", "628.66 ms in get_probes(4)\n", " 37.61 s in load_gse( series_id platform_id..., 4511, False)\n", " 5.30 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27597, id = 4518\n", "541.85 ms in get_probes(280)\n", " 15.73 s in load_gse( series_id platform_id..., 4518, False)\n", " 3.49 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29133, id = 4897\n", "660.30 ms in get_probes(4)\n", " 6.74 s in load_gse( series_id platform_id..., 4897, False)\n", " 2.33 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE30063, id = 5140\n", "629.79 ms in get_probes(4)\n", " 54.94 s in load_gse( series_id platform_id..., 5140, False)\n", "skipping GPL570: sample ids mismatch\n", "193.39 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE37768, id = 6962\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:3083 chronic obstructive pulmonary disease\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE37768/GSE37768_series_matrix.txt.gz ...\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE37768/GSE37768-GPL570_series_matrix.txt.gz ...\n", "Failed loading matrix for serie 6962, platform 4" ] }, { "name": "stderr", "output_type": "stream", "text": [ "631.09 ms in get_probes(4)\n", " 2.21 s in load_gse( series_id platform_id..., 6962, False)\n", "skipping GPL570: sample ids mismatch\n", "154.20 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE47460, id = 9050\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE47460/GSE47460_series_matrix.txt.gz ...\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE47460/GSE47460-GPL14550_series_matrix.txt.gz ...\n", "Cache to" ] }, { "name": "stderr", "output_type": "stream", "text": [ "522.57 ms in get_probes(1010)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " data/geo_mirror/DATA/SeriesMatrix/GSE47460/GSE47460-GPL14550_series_matrix.txt.gz\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE47460/GSE47460_series_matrix.txt.gz ...\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE47460/GSE47460-GPL6480_series_matrix.txt.gz ...\n", "Cache to" ] }, { "name": "stderr", "output_type": "stream", "text": [ "508.03 ms in get_probes(53)\n", " 97.00 s in load_gse( series_id platform_id..., 9050, False)\n", " 21.30 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5058, id = 9577\n", "653.07 ms in get_probes(4)\n", " 21.41 s in load_gse( series_id platform_id..., 9577, False)\n", " 4.34 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54837, id = 10256\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " data/geo_mirror/DATA/SeriesMatrix/GSE47460/GSE47460-GPL6480_series_matrix.txt.gz\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE54837/GSE54837_series_matrix.txt.gz ...\n", "Cache to" ] }, { "name": "stderr", "output_type": "stream", "text": [ "642.78 ms in get_probes(4)\n", "144.53 s in load_gse( series_id platform_id..., 10256, False)\n", " 15.93 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE8545, id = 11509\n", "639.79 ms in get_probes(4)\n", " 30.96 s in load_gse( series_id platform_id..., 11509, False)\n", " 4.14 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE8581, id = 11514\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " data/geo_mirror/DATA/SeriesMatrix/GSE54837/GSE54837_series_matrix.txt.gz\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE8581/GSE8581_series_matrix.txt.gz ...\n", "Cache to" ] }, { "name": "stderr", "output_type": "stream", "text": [ "640.51 ms in get_probes(4)\n", " 38.96 s in load_gse( series_id platform_id..., 11514, False)\n", " 4.06 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27543, id = 11960\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " data/geo_mirror/DATA/SeriesMatrix/GSE8581/GSE8581_series_matrix.txt.gz\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE27543/GSE27543_series_matrix.txt.gz ...\n", "Cache to" ] }, { "name": "stderr", "output_type": "stream", "text": [ "255.21 ms in get_probes(80)\n", " 5.33 s in load_gse( series_id platform_id..., 11960, False)\n", "857.31 ms in get_gene_fold_change(, False, 0, None)\n", "862.71 s in Load/fold for DOID_3083\n", "Meta-Analyzing DOID_3083\n", "430.64 s in meta analysis of real data for DOID_3083\n", " 1.89 s in meta analysis of permutations for DOID_3083\n", "133.99 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "433.13 s in Meta analysis for DOID_3083\n", "DONE DOID_3083 analysis\n", "1297.00 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " data/geo_mirror/DATA/SeriesMatrix/GSE27543/GSE27543_series_matrix.txt.gz\n", "40" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_3310 analysis\n", " 1.11 s in get_analysis_df(\"eczema == 'eczema'\", \"eczema_control == 'ec..., '')\n", " 1.11 s in Loading dataframe for DOID_3310\n", "Matching sources: 8\n", "Excluded 2 sources as single-class\n", "Stats: 6 sources, 5 series, 5 platforms, 129 samples\n", "Loading data and calculating fold change for DOID_3310\n", "Loading data for GSE12511, id = 664\n", "625.27 ms in get_probes(367)\n", " 13.99 s in load_gse( series_id platform_id..., 664, False)\n", " 2.38 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE13709, id = 966\n", "223.48 ms in get_probes(414)\n", "239.09 ms in get_probes(415)\n", " 4.05 s in load_gse( series_id platform_id..., 966, False)\n", " 1.34 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE16161, id = 1619\n", "656.46 ms in get_probes(4)\n", " 15.02 s in load_gse( series_id platform_id..., 1619, False)\n", " 3.03 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE26952, id = 4370\n", "377.51 ms in get_probes(74)\n", " 5.22 s in load_gse( series_id platform_id..., 4370, False)\n", " 1.35 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE32924, id = 5815\n", "628.66 ms in get_probes(4)\n", " 21.82 s in load_gse( series_id platform_id..., 5815, False)\n", " 3.09 s in get_gene_fold_change(, False, 0, None)\n", " 73.07 s in Load/fold for DOID_3310\n", "Meta-Analyzing DOID_3310\n", "400.80 s in meta analysis of real data for DOID_3310\n", "458.33 ms in meta analysis of permutations for DOID_3310\n", "133.99 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "401.87 s in Meta analysis for DOID_3310\n", "DONE DOID_3310 analysis\n", "476.25 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:3310 atopic dermatitis\n", "41" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_3312 analysis\n", " 1.03 s in get_analysis_df(\"bipolar_disorder == '..., \"bipolar_disorder_cont..., '')\n", " 1.04 s in Loading dataframe for DOID_3312\n", "Matching sources: 15\n", "Excluded 6 sources as single-class\n", "Stats: 9 sources, 9 series, 6 platforms, 438 samples\n", "Loading data and calculating fold change for DOID_3312\n", "Loading data for GSE11767, id = 446\n", "392.53 ms in get_probes(9)\n", " 3.94 s in load_gse( series_id platform_id..., 446, False)\n", " 1.30 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE23848, id = 3566\n", "483.47 ms in get_probes(343)\n", " 19.54 s in load_gse( series_id platform_id..., 3566, False)\n", " 2.22 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE39653, id = 7363\n", "711.53 ms in get_probes(674)\n", " 28.19 s in load_gse( series_id platform_id..., 7363, False)\n", " 2.97 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE46449, id = 8868\n", "641.65 ms in get_probes(4)\n", " 59.45 s in load_gse( series_id platform_id..., 8868, False)\n", " 7.30 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5389, id = 10094\n", "394.35 ms in get_probes(2)\n", " 6.97 s in load_gse( series_id platform_id..., 10094, False)\n", " 1.82 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE5392, id = 10102\n", "395.19 ms in get_probes(2)\n", " 22.29 s in load_gse( series_id platform_id..., 10102, False)\n", " 3.42 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE53987, id = 10110\n", "629.34 ms in get_probes(4)\n", " 97.29 s in load_gse( series_id platform_id..., 10110, False)\n", " 8.70 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE7036, id = 11138\n", "623.48 ms in get_probes(4)\n", " 7.56 s in load_gse( series_id platform_id..., 11138, False)\n", " 2.24 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE62191, id = 13125\n", "708.76 ms in get_probes(10)\n", " 33.04 s in load_gse( series_id platform_id..., 13125, False)\n", " 4.11 s in get_gene_fold_change(, False, 0, None)\n", "315.56 s in Load/fold for DOID_3312\n", "Meta-Analyzing DOID_3312\n", "433.85 s in meta analysis of real data for DOID_3312\n", "923.38 ms in meta analysis of permutations for DOID_3312\n", "125.89 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "435.38 s in Meta analysis for DOID_3312\n", "DONE DOID_3312 analysis\n", "752.19 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:3312 bipolar disorder\n", "42" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_332 analysis\n", "851.23 ms in get_analysis_df(\"ALS == 'ALS'\", \"ALS_control == 'ALS_c..., '')\n", "855.41 ms in Loading dataframe for DOID_332\n", "Matching sources: 11\n", "Excluded 1 source as single-class\n", "Stats: 10 sources, 10 series, 7 platforms, 171 samples\n", "Loading data and calculating fold change for DOID_332\n", "Loading data for GSE18920, id = 2315\n", " 4.71 s in get_probes(54)\n", "111.90 s in load_gse( series_id platform_id..., 2315, False)\n", " 35.83 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE19332, id = 2413\n", "632.54 ms in get_probes(4)\n", " 8.82 s in load_gse( series_id platform_id..., 2413, False)\n", " 2.45 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE26276, id = 4160\n", "406.72 ms in get_probes(283)\n", " 6.01 s in load_gse( series_id platform_id..., 4160, False)\n", " 1.42 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE28253, id = 4659\n", "672.36 ms in get_probes(10)\n", " 15.94 s in load_gse( series_id platform_id..., 4659, False)\n", " 2.47 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE33855, id = 6038\n", " 4.88 s in get_probes(54)\n", " 63.26 s in load_gse( series_id platform_id..., 6038, False)\n", " 21.54 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE40328, id = 7530\n", " 40.42 ms in get_probes(643)\n", "984.98 ms in load_gse( series_id platform_id..., 7530, False)\n", "508.12 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE4595, id = 8780\n", "659.16 ms in get_probes(26)\n", " 10.63 s in load_gse( series_id platform_id..., 8780, False)\n", " 2.34 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE56500, id = 10463\n", " 4.89 s in get_probes(54)\n", " 50.09 s in load_gse( series_id platform_id..., 10463, False)\n", " 18.34 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE56808, id = 10498\n", "626.72 ms in get_probes(4)\n", " 12.26 s in load_gse( series_id platform_id..., 10498, False)\n", " 2.29 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE833, id = 11454\n", "299.55 ms in get_probes(22)\n", " 2.16 s in load_gse( series_id platform_id..., 11454, False)\n", "701.36 ms in get_gene_fold_change(, False, 0, None)\n", "377.61 s in Load/fold for DOID_332\n", "Meta-Analyzing DOID_332\n", "451.50 s in meta analysis of real data for DOID_332\n", " 5.83 s in meta analysis of permutations for DOID_332\n", "145.91 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "457.96 s in Meta analysis for DOID_332\n", "DONE DOID_332 analysis\n", "836.62 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:332 amyotrophic lateral sclerosis\n", "43" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_3393 analysis\n", " 1.53 s in get_analysis_df(\"CAD == 'CAD'\", \"CAD_control == 'CAD_c..., '')\n", " 1.53 s in Loading dataframe for DOID_3393\n", "Matching sources: 8\n", "Excluded 1 source as single-class\n", "Stats: 7 sources, 7 series, 6 platforms, 524 samples\n", "Loading data and calculating fold change for DOID_3393\n", "Loading data for GSE10195, id = 57\n", "663.67 ms in get_probes(26)\n", " 24.61 s in load_gse( series_id platform_id..., 57, False)\n", " 3.16 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE12288, id = 598\n", "397.14 ms in get_probes(2)\n", " 42.26 s in load_gse( series_id platform_id..., 598, False)\n", " 7.97 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE18608, id = 2234\n", "763.73 ms in get_probes(4)\n", " 8.59 s in load_gse( series_id platform_id..., 2234, False)\n", " 2.59 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE23561, id = 3492\n", "584.42 ms in get_probes(780)\n", " 17.03 s in load_gse( series_id platform_id..., 3492, False)\n", " 2.25 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE42148, id = 7959\n", "692.92 ms in get_probes(866)\n", " 17.94 s in load_gse( series_id platform_id..., 7959, False)\n", " 3.64 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE7638, id = 11305\n", "391.15 ms in get_probes(9)\n", " 41.36 s in load_gse( series_id platform_id..., 11305, False)\n", " 6.02 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE974, id = 11812\n", "386.98 ms in get_probes(2)\n", " 8.00 s in load_gse( series_id platform_id..., 11812, False)\n", " 2.12 s in get_gene_fold_change(, False, 0, None)\n", "190.06 s in Load/fold for DOID_3393\n", "Meta-Analyzing DOID_3393\n", "415.26 s in meta analysis of real data for DOID_3393\n", "716.08 ms in meta analysis of permutations for DOID_3393\n", "133.04 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "416.59 s in Meta analysis for DOID_3393\n", "DONE DOID_3393 analysis\n", "608.37 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:3393 coronary artery disease\n", "44" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_418 analysis\n", "997.25 ms in get_analysis_df(\"systemic_scleroderma ..., \"systemic_scleroderma_..., '')\n", " 1.00 s in Loading dataframe for DOID_418\n", "Matching sources: 10\n", "Excluded 4 sources as single-class\n", "Excluded 2 sources by min samples\n", "Stats: 4 sources, 4 series, 3 platforms, 157 samples\n", "Loading data and calculating fold change for DOID_418\n", "Loading data for GSE3886, id = 7181\n", "107.55 ms in get_probes(1119)\n", " 6.61 s in load_gse( series_id platform_id..., 7181, False)\n", "493.00 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE4385, id = 8361\n", "106.08 ms in get_probes(1119)\n", " 6.50 s in load_gse( series_id platform_id..., 8361, False)\n", "417.23 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE45536, id = 8688\n", "623.45 ms in get_probes(4)\n", " 56.86 s in load_gse( series_id platform_id..., 8688, False)\n", " 9.42 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE63903, id = 13309\n", "513.58 ms in get_probes(674)\n", " 10.49 s in load_gse( series_id platform_id..., 13309, False)\n", " 2.11 s in get_gene_fold_change(, False, 0, None)\n", " 94.24 s in Load/fold for DOID_418\n", "Meta-Analyzing DOID_418\n", "321.34 s in meta analysis of real data for DOID_418\n", "248.30 ms in meta analysis of permutations for DOID_418\n", "272.04 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper I..., Empty DataFrame Column...)\n", "322.18 s in Meta analysis for DOID_418\n", "DONE DOID_418 analysis\n", "417.61 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:418 systemic scleroderma\n", "45" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_4481 analysis\n", "854.53 ms in get_analysis_df(\"allergic_rhinitis == ..., \"allergic_rhinitis_con..., '')\n", "858.97 ms in Loading dataframe for DOID_4481\n", "Matching sources: 12\n", "Stats: 12 sources, 11 series, 10 platforms, 352 samples\n", "Loading data and calculating fold change for DOID_4481\n", "Loading data for GSE19187, id = 2377\n", "415.71 ms in get_probes(283)\n", " 14.56 s in load_gse( series_id platform_id..., 2377, False)\n", " 2.27 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE1964, id = 2481\n", "112.97 ms in get_probes(654)\n", " 2.30 s in load_gse( series_id platform_id..., 2481, False)\n", "409.70 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE37146, id = 6813\n", "422.10 ms in get_probes(17)\n", " 13.64 s in load_gse( series_id platform_id..., 6813, False)\n", " 2.02 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE37155, id = 6815\n", "510.50 ms in get_probes(674)\n", " 7.58 s in load_gse( series_id platform_id..., 6815, False)\n", " 1.87 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE44037, id = 8399\n", "810.77 ms in get_probes(901)\n", " 21.03 s in load_gse( series_id platform_id..., 8399, False)\n", " 3.12 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE46171, id = 8818\n", "701.67 ms in get_probes(1363)\n", "651.74 ms in get_probes(53)\n", " 42.54 s in load_gse( series_id platform_id..., 8818, False)\n", " 3.91 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE50101, id = 9523\n", "515.88 ms in get_probes(674)\n", " 22.78 s in load_gse( series_id platform_id..., 9523, False)\n", " 3.14 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE50223, id = 9538\n", "479.59 ms in get_probes(416)\n", " 43.85 s in load_gse( series_id platform_id..., 9538, False)\n", " 4.76 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE51392, id = 9724\n", "876.77 ms in get_probes(901)\n", " 38.75 s in load_gse( series_id platform_id..., 9724, False)\n", " 4.32 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE43523, id = 12101\n", "427.12 ms in get_probes(331)\n", " 5.09 s in load_gse( series_id platform_id..., 12101, False)\n", " 1.58 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE54522, id = 12433\n", "621.12 ms in get_probes(4)\n", " 33.04 s in load_gse( series_id platform_id..., 12433, False)\n", " 4.50 s in get_gene_fold_change(, False, 0, None)\n", "281.15 s in Load/fold for DOID_4481\n", "Meta-Analyzing DOID_4481\n", "463.05 s in meta analysis of real data for DOID_4481\n", "914.85 ms in meta analysis of permutations for DOID_4481\n", "109.91 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "464.60 s in Meta analysis for DOID_4481\n", "DONE DOID_4481 analysis\n", "746.82 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:4481 allergic rhinitis\n", "46" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_4606 analysis\n", "883.26 ms in get_analysis_df(\"bile_duct_cancer == '..., \"bile_duct_cancer_cont..., '')\n", "887.41 ms in Loading dataframe for DOID_4606\n", "Matching sources: 0\n", "FAIL Can't perform meta-analysis on no data\n", "950.47 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:4606 bile duct cancer\n", "47" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_5419 analysis\n", "896.83 ms in get_analysis_df(\"schizophrenia == 'sch..., \"Psychiatric_Control =..., '')\n", "901.10 ms in Loading dataframe for DOID_5419\n", "Matching sources: 28\n", "Excluded 4 sources as single-class\n", "Stats: 24 sources, 23 series, 13 platforms, 1486 samples\n", "Loading data and calculating fold change for DOID_5419\n", "Loading data for GSE12649, id = 702\n", "386.06 ms in get_probes(2)\n", " 24.31 s in load_gse( series_id platform_id..., 702, False)\n", " 2.83 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE12654, id = 704\n", "289.12 ms in get_probes(7)\n", " 7.81 s in load_gse( series_id platform_id..., 704, False)\n", " 1.15 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17612, id = 1980\n", "629.49 ms in get_probes(4)\n", " 25.63 s in load_gse( series_id platform_id..., 1980, False)\n", " 4.76 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE18312, id = 2160\n", "529.67 ms in get_probes(280)\n", " 8.04 s in load_gse( series_id platform_id..., 2160, False)\n", " 2.38 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE19112, id = 2359\n", " 40.91 ms in get_probes(643)\n", " 2.27 s in load_gse( series_id platform_id..., 2359, False)\n", "334.33 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE21138, id = 2862\n", "782.95 ms in get_probes(4)\n", " 16.64 s in load_gse( series_id platform_id..., 2862, False)\n", " 4.81 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE21935, id = 3048\n", "618.92 ms in get_probes(4)\n", " 29.96 s in load_gse( series_id platform_id..., 3048, False)\n", " 4.27 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE25673, id = 4035\n", "404.89 ms in get_probes(283)\n", " 9.81 s in load_gse( series_id platform_id..., 4035, False)\n", " 1.95 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27383, id = 4471\n", "615.39 ms in get_probes(4)\n", " 46.80 s in load_gse( series_id platform_id..., 4471, False)\n", " 5.92 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE35974, id = 6545\n", "405.95 ms in get_probes(283)\n", " 46.42 s in load_gse( series_id platform_id..., 6545, False)\n", " 3.92 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE35977, id = 6547\n", "407.10 ms in get_probes(283)\n", " 54.20 s in load_gse( series_id platform_id..., 6547, False)\n", " 4.08 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE37981, id = 7007\n", "686.90 ms in get_probes(67)\n", " 14.75 s in load_gse( series_id platform_id..., 7007, False)\n", " 3.05 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE38481, id = 7104\n", "410.37 ms in get_probes(331)\n", " 11.16 s in load_gse( series_id platform_id..., 7104, False)\n", " 2.21 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE38484, id = 7105\n", "480.04 ms in get_probes(389)\n", "108.52 s in load_gse( series_id platform_id..., 7105, False)\n", " 8.23 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE38485, id = 7106\n", "411.74 ms in get_probes(331)\n", "645.29 ms in get_probes(389)\n", "119.71 s in load_gse( series_id platform_id..., 7106, False)\n", " 10.31 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE46509, id = 8882\n", "685.77 ms in get_probes(67)\n", " 13.58 s in load_gse( series_id platform_id..., 8882, False)\n", " 2.91 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE48072, id = 9177\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:5419 schizophrenia\n", "Loading URL ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE48072/GSE48072_series_matrix.txt.gz ...\n", "Cache to" ] }, { "name": "stderr", "output_type": "stream", "text": [ "519.99 ms in get_probes(674)\n", " 5.68 s in load_gse( series_id platform_id..., 9177, False)\n", " 2.79 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE53987, id = 10110\n", "632.76 ms in get_probes(4)\n", " 97.32 s in load_gse( series_id platform_id..., 10110, False)\n", " 7.77 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27356, id = 11959\n", " 38.72 ms in get_probes(1703)\n", " 1.59 s in load_gse( series_id platform_id..., 11959, False)\n", "259.60 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27601, id = 11963\n", " 38.98 ms in get_probes(1703)\n", " 1.38 s in load_gse( series_id platform_id..., 11963, False)\n", "173.81 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE62105, id = 13113\n", "658.87 ms in get_probes(10)\n", " 9.42 s in load_gse( series_id platform_id..., 13113, False)\n", " 1.97 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE62191, id = 13125\n", "656.88 ms in get_probes(10)\n", " 31.80 s in load_gse( series_id platform_id..., 13125, False)\n", " 3.92 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE62333, id = 13140\n", "412.48 ms in get_probes(953)\n", " 16.61 s in load_gse( series_id platform_id..., 13140, False)\n", " 2.33 s in get_gene_fold_change(, False, 0, None)\n", "795.01 s in Load/fold for DOID_5419\n", "Meta-Analyzing DOID_5419\n", "470.79 s in meta analysis of real data for DOID_5419\n", " 1.72 s in meta analysis of permutations for DOID_5419\n", "107.05 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "473.12 s in Meta analysis for DOID_5419\n", "DONE DOID_5419 analysis\n", "1269.32 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " data/geo_mirror/DATA/SeriesMatrix/GSE48072/GSE48072_series_matrix.txt.gz\n", "48" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_635 analysis\n", " 1.52 s in get_analysis_df(\"HIV == 'HIV' or HIV_S..., \"HIV_control == 'HIV_c..., '')\n", " 1.53 s in Loading dataframe for DOID_635\n", "Matching sources: 27\n", "Excluded 3 sources as single-class\n", "Excluded 2 sources by min samples\n", "Stats: 22 sources, 22 series, 13 platforms, 1973 samples\n", "Loading data and calculating fold change for DOID_635\n", "Loading data for GSE12597, id = 683\n", " 41.88 ms in get_probes(370)\n", "275.58 ms in load_gse( series_id platform_id..., 683, False)\n", "304.20 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE14542, id = 1175\n", " 43.77 ms in get_probes(454)\n", " 6.33 s in load_gse( series_id platform_id..., 1175, False)\n", "350.76 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE16363, id = 1658\n", "628.50 ms in get_probes(4)\n", " 25.98 s in load_gse( series_id platform_id..., 1658, False)\n", " 4.82 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE18233, id = 2140\n", "487.55 ms in get_probes(416)\n", "109.28 s in load_gse( series_id platform_id..., 2140, False)\n", " 8.96 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE19811, id = 2535\n", "390.61 ms in get_probes(2)\n", " 5.61 s in load_gse( series_id platform_id..., 2535, False)\n", " 1.46 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE28177, id = 4638\n", "623.44 ms in get_probes(4)\n", " 7.01 s in load_gse( series_id platform_id..., 4638, False)\n", " 2.18 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE28944, id = 4847\n", "111.59 ms in get_probes(929)\n", "453.37 ms in load_gse( series_id platform_id..., 4847, False)\n", "353.63 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29536, id = 4997\n", "428.85 ms in get_probes(17)\n", "181.82 s in load_gse( series_id platform_id..., 4997, False)\n", " 6.11 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29939, id = 5106\n", "111.79 ms in get_probes(929)\n", "776.25 ms in load_gse( series_id platform_id..., 5106, False)\n", "437.36 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE30310, id = 5201\n", "191.56 ms in get_probes(616)\n", " 8.27 s in load_gse( series_id platform_id..., 5201, False)\n", " 1.16 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE33877, id = 6044\n", "493.67 ms in get_probes(389)\n", " 8.24 s in load_gse( series_id platform_id..., 6044, False)\n", " 1.85 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE3489, id = 6268\n", "291.86 ms in get_probes(7)\n", " 3.81 s in load_gse( series_id platform_id..., 6268, False)\n", " 1.17 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE35864, id = 6523\n", "624.01 ms in get_probes(4)\n", " 47.44 s in load_gse( series_id platform_id..., 6523, False)\n", " 5.88 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE37250, id = 6847\n", "515.67 ms in get_probes(674)\n", "251.80 s in load_gse( series_id platform_id..., 6847, False)\n", " 25.40 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE39939, id = 7430\n", "513.91 ms in get_probes(674)\n", " 74.90 s in load_gse( series_id platform_id..., 7430, False)\n", " 8.27 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE39940, id = 7431\n", "522.92 ms in get_probes(674)\n", "158.48 s in load_gse( series_id platform_id..., 7431, False)\n", " 15.82 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE4124, id = 7745\n", "391.93 ms in get_probes(9)\n", " 8.47 s in load_gse( series_id platform_id..., 7745, False)\n", " 2.23 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE42058, id = 7937\n", "669.49 ms in get_probes(4)\n", " 7.46 s in load_gse( series_id platform_id..., 7937, False)\n", " 2.28 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE511, id = 9682\n", "218.15 ms in get_probes(22)\n", " 4.04 s in load_gse( series_id platform_id..., 9682, False)\n", "805.11 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE52900, id = 9963\n", "493.58 ms in get_probes(389)\n", " 11.16 s in load_gse( series_id platform_id..., 9963, False)\n", " 1.45 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6740, id = 11026\n", "391.92 ms in get_probes(2)\n", " 14.59 s in load_gse( series_id platform_id..., 11026, False)\n", " 2.17 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE9927, id = 11872\n", "619.32 ms in get_probes(4)\n", " 12.15 s in load_gse( series_id platform_id..., 11872, False)\n", " 2.95 s in get_gene_fold_change(, False, 0, None)\n", "1053.46 s in Load/fold for DOID_635\n", "Meta-Analyzing DOID_635\n", "468.17 s in meta analysis of real data for DOID_635\n", " 1.32 s in meta analysis of permutations for DOID_635\n", "106.10 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "470.09 s in Meta analysis for DOID_635\n", "DONE DOID_635 analysis\n", "1525.38 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:635 acquired immunodeficiency syndrome\n", "49" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_7147 analysis\n", " 1.03 s in get_analysis_df(\"ankylosing_spondyliti..., \"ankylosing_spondyliti..., '')\n", " 1.03 s in Loading dataframe for DOID_7147\n", "Matching sources: 3\n", "Excluded 1 source by min samples\n", "Stats: 2 sources, 2 series, 2 platforms, 65 samples\n", "Loading data and calculating fold change for DOID_7147\n", "Loading data for GSE11886, id = 479\n", "638.99 ms in get_probes(4)\n", " 22.72 s in load_gse( series_id platform_id..., 479, False)\n", " 3.68 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE25101, id = 3902\n", "513.57 ms in get_probes(389)\n", " 7.90 s in load_gse( series_id platform_id..., 3902, False)\n", " 2.11 s in get_gene_fold_change(, False, 0, None)\n", " 37.20 s in Load/fold for DOID_7147\n", "Meta-Analyzing DOID_7147\n", "207.42 s in meta analysis of real data for DOID_7147\n", "200.72 ms in meta analysis of permutations for DOID_7147\n", "106.10 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper I..., Empty DataFrame Column...)\n", "208.24 s in Meta analysis for DOID_7147\n", "DONE DOID_7147 analysis\n", "246.64 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:7147 ankylosing spondylitis\n", "50" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_7148 analysis\n", "853.14 ms in get_analysis_df(\"RA == 'RA'\", \"RA_control == 'RA_con..., '')\n", "857.36 ms in Loading dataframe for DOID_7148\n", "Matching sources: 21\n", "Excluded 1 source as single-class\n", "Excluded 2 sources by min samples\n", "Stats: 18 sources, 17 series, 13 platforms, 607 samples\n", "Loading data and calculating fold change for DOID_7148\n", "Loading data for GSE10500, id = 137\n", "289.59 ms in get_probes(7)\n", " 2.22 s in load_gse( series_id platform_id..., 137, False)\n", "855.79 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE11827, id = 457\n", " 38.24 ms in get_probes(36)\n", " 8.78 s in load_gse( series_id platform_id..., 457, False)\n", "199.79 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE12021, id = 517\n", "380.47 ms in get_probes(2)\n", "343.15 ms in get_probes(50)\n", " 14.78 s in load_gse( series_id platform_id..., 517, False)\n", " 2.69 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE13026, id = 799\n", " 37.97 ms in get_probes(36)\n", " 7.97 s in load_gse( series_id platform_id..., 799, False)\n", "193.79 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE15573, id = 1473\n", "445.99 ms in get_probes(17)\n", " 17.80 s in load_gse( series_id platform_id..., 1473, False)\n", " 2.33 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17755, id = 2014\n", "326.36 ms in get_probes(51)\n", " 52.01 s in load_gse( series_id platform_id..., 2014, False)\n", " 3.89 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE1919, id = 2379\n", "288.36 ms in get_probes(8)\n", " 2.67 s in load_gse( series_id platform_id..., 2379, False)\n", "928.61 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE2053, id = 2720\n", "225.81 ms in get_probes(688)\n", " 2.36 s in load_gse( series_id platform_id..., 2720, False)\n", "635.11 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE21959, id = 3055\n", "655.44 ms in get_probes(10)\n", " 17.50 s in load_gse( series_id platform_id..., 3055, False)\n", " 3.05 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE23561, id = 3492\n", "558.63 ms in get_probes(780)\n", " 16.56 s in load_gse( series_id platform_id..., 3492, False)\n", " 2.10 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29746, id = 5051\n", "666.97 ms in get_probes(10)\n", " 15.31 s in load_gse( series_id platform_id..., 5051, False)\n", " 1.83 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE4588, id = 8761\n", "622.37 ms in get_probes(4)\n", " 23.64 s in load_gse( series_id platform_id..., 8761, False)\n", " 3.66 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE49604, id = 9430\n", "519.46 ms in get_probes(674)\n", " 9.56 s in load_gse( series_id platform_id..., 9430, False)\n", " 1.98 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE55235, id = 10308\n", "392.68 ms in get_probes(2)\n", " 6.79 s in load_gse( series_id platform_id..., 10308, False)\n", " 1.63 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE55457, id = 10327\n", "385.98 ms in get_probes(2)\n", " 7.25 s in load_gse( series_id platform_id..., 10327, False)\n", " 1.68 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE57383, id = 12627\n", "643.29 ms in get_probes(901)\n", " 54.60 s in load_gse( series_id platform_id..., 12627, False)\n", " 4.34 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE57405, id = 12629\n", "644.98 ms in get_probes(901)\n", " 53.72 s in load_gse( series_id platform_id..., 12629, False)\n", " 4.33 s in get_gene_fold_change(, False, 0, None)\n", "355.39 s in Load/fold for DOID_7148\n", "Meta-Analyzing DOID_7148\n", "457.07 s in meta analysis of real data for DOID_7148\n", " 1.07 s in meta analysis of permutations for DOID_7148\n", " 99.90 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "458.75 s in Meta analysis for DOID_7148\n", "DONE DOID_7148 analysis\n", "815.24 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:7148 rheumatoid arthritis\n", "51" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_7693 analysis\n", "950.53 ms in get_analysis_df(\"AAA == 'AAA'\", \"AAA_control == 'AAA_c..., '')\n", "954.72 ms in Loading dataframe for DOID_7693\n", "Matching sources: 5\n", "Excluded 1 source by min samples\n", "Stats: 4 sources, 4 series, 3 platforms, 104 samples\n", "Loading data and calculating fold change for DOID_7693\n", "Loading data for GSE21803, id = 3020\n", " 76.31 ms in get_probes(724)\n", "409.19 ms in load_gse( series_id platform_id..., 3020, False)\n", "313.65 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE47472, id = 9057\n", "670.53 ms in get_probes(674)\n", " 12.07 s in load_gse( series_id platform_id..., 9057, False)\n", " 2.43 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE7084, id = 11146\n", "378.98 ms in get_probes(39)\n", " 9.60 s in load_gse( series_id platform_id..., 11146, False)\n", " 1.43 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE57691, id = 12645\n", "732.48 ms in get_probes(674)\n", " 31.18 s in load_gse( series_id platform_id..., 12645, False)\n", " 3.91 s in get_gene_fold_change(, False, 0, None)\n", " 62.60 s in Load/fold for DOID_7693\n", "Meta-Analyzing DOID_7693\n", "367.08 s in meta analysis of real data for DOID_7693\n", "226.05 ms in meta analysis of permutations for DOID_7693\n", "103.95 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "367.89 s in Meta analysis for DOID_7693\n", "DONE DOID_7693 analysis\n", "431.62 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:7693 abdominal aortic aneurysm\n", "52" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_784 analysis\n", "717.48 ms in get_analysis_df(\"CKD == 'CKD'\", \"CKD_Control == 'CKD_C..., '')\n", "722.02 ms in Loading dataframe for DOID_784\n", "Matching sources: 2\n", "Excluded 1 source as single-class\n", "FAIL Can't perform meta-analysis on single source\n", "857.18 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:784 chronic kidney failure\n", "53" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_824 analysis\n", "522.07 ms in get_analysis_df(\"periodontitis == 'per..., \"periodontitis_control..., '')\n", "526.46 ms in Loading dataframe for DOID_824\n", "Matching sources: 3\n", "Excluded 1 source by min samples\n", "Stats: 2 sources, 2 series, 2 platforms, 33 samples\n", "Loading data and calculating fold change for DOID_824\n", "Loading data for GSE27993, id = 4587\n", "404.76 ms in get_probes(283)\n", " 6.12 s in load_gse( series_id platform_id..., 4587, False)\n", " 1.47 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE43525, id = 8303\n", "514.93 ms in get_probes(674)\n", " 15.08 s in load_gse( series_id platform_id..., 8303, False)\n", " 2.45 s in get_gene_fold_change(, False, 0, None)\n", " 25.61 s in Load/fold for DOID_824\n", "Meta-Analyzing DOID_824\n", "324.19 s in meta analysis of real data for DOID_824\n", "152.86 ms in meta analysis of permutations for DOID_824\n", "108.00 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper I..., Empty DataFrame Column...)\n", "324.99 s in Meta analysis for DOID_824\n", "DONE DOID_824 analysis\n", "351.29 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:824 periodontitis\n", "54" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_8577 analysis\n", "779.32 ms in get_analysis_df(\"UC == 'UC'\", \"UC_control == 'UC_con..., '')\n", "783.89 ms in Loading dataframe for DOID_8577\n", "Matching sources: 18\n", "Excluded 1 source as single-class\n", "Stats: 17 sources, 17 series, 12 platforms, 838 samples\n", "Loading data and calculating fold change for DOID_8577\n", "Loading data for GSE10191, id = 56\n", "402.45 ms in get_probes(25)\n", " 7.95 s in load_gse( series_id platform_id..., 56, False)\n", " 1.68 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE10616, id = 169\n", "401.80 ms in get_probes(25)\n", " 16.80 s in load_gse( series_id platform_id..., 169, False)\n", " 1.71 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE11223, id = 317\n", "637.65 ms in get_probes(26)\n", " 77.71 s in load_gse( series_id platform_id..., 317, False)\n", " 10.00 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE1710, id = 1852\n", "360.75 ms in get_probes(18)\n", " 15.28 s in load_gse( series_id platform_id..., 1852, False)\n", " 1.41 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE22619, id = 3258\n", "620.39 ms in get_probes(4)\n", " 11.61 s in load_gse( series_id platform_id..., 3258, False)\n", " 2.85 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE24287, id = 3687\n", "499.01 ms in get_probes(53)\n", " 31.25 s in load_gse( series_id platform_id..., 3687, False)\n", " 3.46 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE2461, id = 3778\n", "383.07 ms in get_probes(2)\n", " 2.80 s in load_gse( series_id platform_id..., 3778, False)\n", " 1.25 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE3365, id = 5991\n", "385.28 ms in get_probes(2)\n", " 29.58 s in load_gse( series_id platform_id..., 5991, False)\n", " 2.92 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE36807, id = 6726\n", "619.11 ms in get_probes(4)\n", " 24.55 s in load_gse( series_id platform_id..., 6726, False)\n", " 3.16 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE38713, id = 7147\n", "611.67 ms in get_probes(4)\n", " 29.65 s in load_gse( series_id platform_id..., 7147, False)\n", " 4.28 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6731, id = 11023\n", "288.17 ms in get_probes(7)\n", " 5.00 s in load_gse( series_id platform_id..., 11023, False)\n", "971.40 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE9452, id = 11743\n", "633.45 ms in get_probes(4)\n", " 14.23 s in load_gse( series_id platform_id..., 11743, False)\n", " 2.56 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE42911, id = 12095\n", "635.22 ms in get_probes(1132)\n", " 10.62 s in load_gse( series_id platform_id..., 12095, False)\n", " 2.30 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE48634, id = 12194\n", "524.40 ms in get_probes(674)\n", " 50.54 s in load_gse( series_id platform_id..., 12194, False)\n", " 6.66 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE53306, id = 12370\n", "487.80 ms in get_probes(912)\n", " 13.12 s in load_gse( series_id platform_id..., 12370, False)\n", " 2.97 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE59071, id = 12790\n", "404.84 ms in get_probes(283)\n", " 43.87 s in load_gse( series_id platform_id..., 12790, False)\n", " 4.36 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE65114, id = 13436\n", "352.01 ms in get_probes(1338)\n", " 17.99 s in load_gse( series_id platform_id..., 13436, False)\n", " 1.66 s in get_gene_fold_change(, False, 0, None)\n", "462.60 s in Load/fold for DOID_8577\n", "Meta-Analyzing DOID_8577\n", "457.34 s in meta analysis of real data for DOID_8577\n", " 1.31 s in meta analysis of permutations for DOID_8577\n", "108.96 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "459.25 s in Meta analysis for DOID_8577\n", "DONE DOID_8577 analysis\n", "922.87 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:8577 ulcerative colitis\n", "55" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_8778 analysis\n", " 1.14 s in get_analysis_df(\"CD == 'CD'\", \"CD_control == 'CD_con..., '')\n", " 1.14 s in Loading dataframe for DOID_8778\n", "Matching sources: 20\n", "Excluded 1 source as single-class\n", "Excluded 7 sources by min samples\n", "Stats: 12 sources, 12 series, 11 platforms, 743 samples\n", "Loading data and calculating fold change for DOID_8778\n", "Loading data for GSE10616, id = 169\n", "398.22 ms in get_probes(25)\n", " 17.10 s in load_gse( series_id platform_id..., 169, False)\n", " 2.46 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE1710, id = 1852\n", "348.71 ms in get_probes(18)\n", " 15.16 s in load_gse( series_id platform_id..., 1852, False)\n", " 1.42 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17594, id = 1976\n", "632.79 ms in get_probes(10)\n", " 2.49 s in load_gse( series_id platform_id..., 1976, False)\n", " 2.12 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20881, id = 2803\n", "635.53 ms in get_probes(26)\n", " 61.36 s in load_gse( series_id platform_id..., 2803, False)\n", " 8.74 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE24287, id = 3687\n", "504.27 ms in get_probes(53)\n", " 31.14 s in load_gse( series_id platform_id..., 3687, False)\n", " 4.27 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE3365, id = 5991\n", "381.30 ms in get_probes(2)\n", " 29.52 s in load_gse( series_id platform_id..., 5991, False)\n", " 3.83 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE36807, id = 6726\n", "612.43 ms in get_probes(4)\n", " 24.01 s in load_gse( series_id platform_id..., 6726, False)\n", " 2.98 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE52746, id = 9944\n", "364.48 ms in get_probes(1438)\n", " 6.94 s in load_gse( series_id platform_id..., 9944, False)\n", " 1.99 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE60083, id = 10812\n", "473.05 ms in get_probes(416)\n", " 12.47 s in load_gse( series_id platform_id..., 10812, False)\n", " 4.15 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6731, id = 11023\n", "287.74 ms in get_probes(7)\n", " 5.00 s in load_gse( series_id platform_id..., 11023, False)\n", " 1.02 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE9686, id = 11793\n", "411.68 ms in get_probes(25)\n", " 10.53 s in load_gse( series_id platform_id..., 11793, False)\n", " 1.96 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE48634, id = 12194\n", "527.24 ms in get_probes(674)\n", " 50.03 s in load_gse( series_id platform_id..., 12194, False)\n", " 4.81 s in get_gene_fold_change(, False, 0, None)\n", "308.64 s in Load/fold for DOID_8778\n", "Meta-Analyzing DOID_8778\n", "411.59 s in meta analysis of real data for DOID_8778\n", "834.50 ms in meta analysis of permutations for DOID_8778\n", "123.02 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "413.03 s in Meta analysis for DOID_8778\n", "DONE DOID_8778 analysis\n", "723.06 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:8778 Crohn's disease\n", "56" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_8893 analysis\n", "955.27 ms in get_analysis_df(\"psoriasis == 'psorias..., \"psoriasis_control == ..., '')\n", "959.42 ms in Loading dataframe for DOID_8893\n", "Matching sources: 11\n", "Excluded 2 sources as single-class\n", "Excluded 1 source by min samples\n", "Stats: 8 sources, 8 series, 7 platforms, 429 samples\n", "Loading data and calculating fold change for DOID_8893\n", "Loading data for GSE13355, id = 878\n", "623.07 ms in get_probes(4)\n", " 94.43 s in load_gse( series_id platform_id..., 878, False)\n", " 7.56 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE32407, id = 5703\n", "390.81 ms in get_probes(9)\n", " 14.97 s in load_gse( series_id platform_id..., 5703, False)\n", " 2.58 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE47598, id = 9087\n", "597.05 ms in get_probes(674)\n", " 15.37 s in load_gse( series_id platform_id..., 9087, False)\n", " 2.52 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE57225, id = 10556\n", "665.53 ms in get_probes(1010)\n", " 31.70 s in load_gse( series_id platform_id..., 10556, False)\n", " 3.01 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE57383, id = 12627\n", "644.49 ms in get_probes(901)\n", " 54.00 s in load_gse( series_id platform_id..., 12627, False)\n", " 4.51 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE57405, id = 12629\n", "647.41 ms in get_probes(901)\n", " 53.04 s in load_gse( series_id platform_id..., 12629, False)\n", " 4.10 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE61281, id = 12998\n", "731.54 ms in get_probes(53)\n", " 27.77 s in load_gse( series_id platform_id..., 12998, False)\n", " 2.78 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE63741, id = 13298\n", " 42.53 ms in get_probes(1794)\n", " 2.58 s in load_gse( series_id platform_id..., 13298, False)\n", "205.63 ms in get_gene_fold_change(, False, 0, None)\n", "323.77 s in Load/fold for DOID_8893\n", "Meta-Analyzing DOID_8893\n", "443.27 s in meta analysis of real data for DOID_8893\n", "638.21 ms in meta analysis of permutations for DOID_8893\n", "106.81 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "444.53 s in Meta analysis for DOID_8893\n", "DONE DOID_8893 analysis\n", "769.45 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:8893 psoriasis\n", "57" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_8986 analysis\n", "726.99 ms in get_analysis_df(\"narcolepsy == 'narcol..., \"narcolepsy_control ==..., '')\n", "731.35 ms in Loading dataframe for DOID_8986\n", "Matching sources: 1\n", "FAIL Can't perform meta-analysis on single source\n", "862.07 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:8986 narcolepsy\n", "58" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_9008 analysis\n", "668.21 ms in get_analysis_df(\"PsA == 'PsA'\", \"PsA_control == 'PsA_c..., '')\n", "672.32 ms in Loading dataframe for DOID_9008\n", "Matching sources: 3\n", "Stats: 3 sources, 3 series, 2 platforms, 141 samples\n", "Loading data and calculating fold change for DOID_9008\n", "Loading data for GSE57383, id = 12627\n", "651.33 ms in get_probes(901)\n", " 54.14 s in load_gse( series_id platform_id..., 12627, False)\n", " 4.85 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE57405, id = 12629\n", "651.99 ms in get_probes(901)\n", " 53.32 s in load_gse( series_id platform_id..., 12629, False)\n", " 4.81 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE61281, id = 12998\n", "693.55 ms in get_probes(53)\n", " 26.74 s in load_gse( series_id platform_id..., 12998, False)\n", " 2.77 s in get_gene_fold_change(, False, 0, None)\n", "147.75 s in Load/fold for DOID_9008\n", "Meta-Analyzing DOID_9008\n", "393.35 s in meta analysis of real data for DOID_9008\n", "313.61 ms in meta analysis of permutations for DOID_9008\n", "109.91 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "394.26 s in Meta analysis for DOID_9008\n", "DONE DOID_9008 analysis\n", "542.85 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:9008 psoriatic arthritis\n", "59" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_9074 analysis\n", "994.35 ms in get_analysis_df(\"SLE == 'SLE'\", \"SLE_control == 'SLE_c..., '')\n", "998.59 ms in Loading dataframe for DOID_9074\n", "Matching sources: 23\n", "Excluded 3 sources as single-class\n", "Excluded 1 source by min samples\n", "Stats: 19 sources, 18 series, 12 platforms, 1375 samples\n", "Loading data and calculating fold change for DOID_9074\n", "Loading data for GSE10325, id = 92\n", "397.73 ms in get_probes(2)\n", " 12.88 s in load_gse( series_id platform_id..., 92, False)\n", " 2.92 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE11907, id = 488\n", "387.36 ms in get_probes(2)\n", "338.73 ms in get_probes(50)\n", " 94.71 s in load_gse( series_id platform_id..., 488, False)\n", " 6.01 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE12374, id = 618\n", "326.56 ms in get_probes(51)\n", " 5.63 s in load_gse( series_id platform_id..., 618, False)\n", " 1.27 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE17755, id = 2014\n", "324.90 ms in get_probes(51)\n", " 51.63 s in load_gse( series_id platform_id..., 2014, False)\n", " 2.25 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20864, id = 2798\n", "327.71 ms in get_probes(51)\n", " 15.96 s in load_gse( series_id platform_id..., 2798, False)\n", " 2.07 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE21649, id = 2983\n", "346.13 ms in get_probes(720)\n", " 4.40 s in load_gse( series_id platform_id..., 2983, False)\n", " 1.17 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE22098, id = 3098\n", "485.52 ms in get_probes(389)\n", "135.92 s in load_gse( series_id platform_id..., 3098, False)\n", " 8.71 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE23203, id = 3404\n", "351.27 ms in get_probes(774)\n", " 7.92 s in load_gse( series_id platform_id..., 3404, False)\n", " 1.65 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27427, id = 4483\n", "446.01 ms in get_probes(343)\n", " 21.41 s in load_gse( series_id platform_id..., 4483, False)\n", " 2.58 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29536, id = 4997\n", "416.49 ms in get_probes(17)\n", "177.81 s in load_gse( series_id platform_id..., 4997, False)\n", " 7.72 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE30153, id = 5158\n", "784.15 ms in get_probes(4)\n", " 12.35 s in load_gse( series_id platform_id..., 5158, False)\n", " 3.08 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE37356, id = 6873\n", "508.06 ms in get_probes(674)\n", " 31.03 s in load_gse( series_id platform_id..., 6873, False)\n", " 4.46 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE4588, id = 8761\n", "638.26 ms in get_probes(4)\n", " 23.10 s in load_gse( series_id platform_id..., 8761, False)\n", " 3.65 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE50395, id = 9551\n", "681.78 ms in get_probes(10)\n", " 9.00 s in load_gse( series_id platform_id..., 9551, False)\n", " 1.78 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE50635, id = 9591\n", "403.44 ms in get_probes(283)\n", " 17.18 s in load_gse( series_id platform_id..., 9591, False)\n", " 2.57 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE51997, id = 9826\n", "623.68 ms in get_probes(4)\n", " 21.57 s in load_gse( series_id platform_id..., 9826, False)\n", " 3.91 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE8650, id = 11535\n", "326.88 ms in get_probes(50)\n", " 22.49 s in load_gse( series_id platform_id..., 11535, False)\n", " 2.05 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE55447, id = 12480\n", "669.90 ms in get_probes(674)\n", " 65.70 s in load_gse( series_id platform_id..., 12480, False)\n", " 7.39 s in get_gene_fold_change(, False, 0, None)\n", "801.76 s in Load/fold for DOID_9074\n", "Meta-Analyzing DOID_9074\n", "469.04 s in meta analysis of real data for DOID_9074\n", " 1.28 s in meta analysis of permutations for DOID_9074\n", " 23.13 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "470.61 s in Meta analysis for DOID_9074\n", "DONE DOID_9074 analysis\n", "1273.63 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:9074 systemic lupus erythematosus\n", "60" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_9206 analysis\n", " 1.01 s in get_analysis_df(\"BE_Tissue == 'BE_Tiss..., \"EAC_Non_Tumor == 'EAC..., '')\n", " 1.01 s in Loading dataframe for DOID_9206\n", "Matching sources: 16\n", "Excluded 10 sources as single-class\n", "Excluded 2 sources by min samples\n", "Stats: 4 sources, 4 series, 3 platforms, 155 samples\n", "Loading data and calculating fold change for DOID_9206\n", "Loading data for GSE34619, id = 6215\n", "407.37 ms in get_probes(283)\n", " 9.69 s in load_gse( series_id platform_id..., 6215, False)\n", " 1.54 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE36223, id = 6608\n", "406.23 ms in get_probes(9)\n", " 6.31 s in load_gse( series_id platform_id..., 6608, False)\n", " 2.12 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE39491, id = 7332\n", "392.33 ms in get_probes(9)\n", " 26.65 s in load_gse( series_id platform_id..., 7332, False)\n", " 3.21 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6059, id = 10854\n", " 75.98 ms in get_probes(1512)\n", " 8.63 s in load_gse( series_id platform_id..., 10854, False)\n", "372.52 ms in get_gene_fold_change(, False, 0, None)\n", " 59.74 s in Load/fold for DOID_9206\n", "Meta-Analyzing DOID_9206\n", "246.52 s in meta analysis of real data for DOID_9206\n", "184.46 ms in meta analysis of permutations for DOID_9206\n", "165.94 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "247.31 s in Meta analysis for DOID_9206\n", "DONE DOID_9206 analysis\n", "308.24 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:9206 Barrett's esophagus\n", "61" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_9296 analysis\n", "661.29 ms in get_analysis_df(\"cleft_lip == 'cleft_l..., \"cleft_lip_control == ..., '')\n", "665.78 ms in Loading dataframe for DOID_9296\n", "Matching sources: 1\n", "FAIL Can't perform meta-analysis on single source\n", "797.02 ms in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:9296 cleft lip\n", "62" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_9352 analysis\n", "733.37 ms in get_analysis_df(\"T2D == 'T2D'\", \"T2D_control == 'T2D_c..., '')\n", "737.53 ms in Loading dataframe for DOID_9352\n", "Matching sources: 36\n", "Excluded 4 sources as single-class\n", "Excluded 1 source by min samples\n", "Stats: 31 sources, 25 series, 19 platforms, 854 samples\n", "Loading data and calculating fold change for DOID_9352\n", "Loading data for GSE121, id = 539\n", "208.38 ms in get_probes(338)\n", "214.39 ms in get_probes(339)\n", "208.06 ms in get_probes(22)\n", "246.73 ms in get_probes(340)\n", "199.74 ms in get_probes(341)\n", " 10.95 s in load_gse( series_id platform_id..., 539, False)\n", " 2.39 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE12643, id = 697\n", "281.04 ms in get_probes(7)\n", " 3.92 s in load_gse( series_id platform_id..., 697, False)\n", " 1.03 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE13015, id = 796\n", "460.82 ms in get_probes(343)\n", "480.53 ms in get_probes(389)\n", " 57.75 s in load_gse( series_id platform_id..., 796, False)\n", " 2.56 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE13760, id = 979\n", "384.94 ms in get_probes(9)\n", " 6.80 s in load_gse( series_id platform_id..., 979, False)\n", " 1.69 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE15653, id = 1495\n", "381.04 ms in get_probes(2)\n", " 5.29 s in load_gse( series_id platform_id..., 1495, False)\n", " 1.49 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE15790, id = 1522\n", "340.33 ms in get_probes(511)\n", " 8.70 s in load_gse( series_id platform_id..., 1522, False)\n", " 1.82 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE16415, id = 1671\n", "347.86 ms in get_probes(60)\n", " 6.69 s in load_gse( series_id platform_id..., 1671, False)\n", " 1.27 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE18732, id = 2269\n", " 38.28 ms in get_probes(628)\n", " 34.60 s in load_gse( series_id platform_id..., 2269, False)\n", "262.89 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE19420, id = 2433\n", "616.83 ms in get_probes(4)\n", " 26.92 s in load_gse( series_id platform_id..., 2433, False)\n", " 3.92 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE20966, id = 2827\n", "694.88 ms in get_probes(67)\n", " 14.18 s in load_gse( series_id platform_id..., 2827, False)\n", " 3.19 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE21340, id = 2908\n", "213.47 ms in get_probes(22)\n", " 2.11 s in load_gse( series_id platform_id..., 2908, False)\n", "657.35 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE23561, id = 3492\n", "560.53 ms in get_probes(780)\n", " 16.12 s in load_gse( series_id platform_id..., 3492, False)\n", " 2.15 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE25462, id = 3991\n", "622.34 ms in get_probes(4)\n", " 24.99 s in load_gse( series_id platform_id..., 3991, False)\n", " 4.66 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE25724, id = 4042\n", "386.42 ms in get_probes(2)\n", " 4.49 s in load_gse( series_id platform_id..., 4042, False)\n", " 1.46 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE26887, id = 4348\n", "404.95 ms in get_probes(283)\n", " 8.31 s in load_gse( series_id platform_id..., 4348, False)\n", " 1.54 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE27949, id = 4577\n", "620.70 ms in get_probes(4)\n", " 22.79 s in load_gse( series_id platform_id..., 4577, False)\n", " 3.14 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29221, id = 4919\n", "488.57 ms in get_probes(389)\n", " 14.63 s in load_gse( series_id platform_id..., 4919, False)\n", " 2.35 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29226, id = 4921\n", "510.62 ms in get_probes(389)\n", " 15.18 s in load_gse( series_id platform_id..., 4921, False)\n", " 2.38 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29231, id = 4922\n", "486.68 ms in get_probes(389)\n", " 14.96 s in load_gse( series_id platform_id..., 4922, False)\n", " 2.37 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE38396, id = 7091\n", "622.50 ms in get_probes(4)\n", " 9.03 s in load_gse( series_id platform_id..., 7091, False)\n", " 2.26 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE38642, id = 7132\n", "406.77 ms in get_probes(283)\n", " 9.89 s in load_gse( series_id platform_id..., 7132, False)\n", " 2.85 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE40234, id = 7508\n", "634.00 ms in get_probes(53)\n", " 28.07 s in load_gse( series_id platform_id..., 7508, False)\n", " 3.90 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE50397, id = 9552\n", "414.24 ms in get_probes(283)\n", " 24.14 s in load_gse( series_id platform_id..., 9552, False)\n", " 3.70 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE6798, id = 11053\n", "620.37 ms in get_probes(4)\n", " 20.94 s in load_gse( series_id platform_id..., 11053, False)\n", " 3.54 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE9006, id = 11628\n", "387.06 ms in get_probes(2)\n", "334.37 ms in get_probes(50)\n", " 43.65 s in load_gse( series_id platform_id..., 11628, False)\n", " 3.51 s in get_gene_fold_change(, False, 0, None)\n", "503.70 s in Load/fold for DOID_9352\n", "Meta-Analyzing DOID_9352\n", "476.91 s in meta analysis of real data for DOID_9352\n", " 1.93 s in meta analysis of permutations for DOID_9352\n", "108.96 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "479.44 s in Meta analysis for DOID_9352\n", "DONE DOID_9352 analysis\n", "984.21 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:9352 type 2 diabetes mellitus\n", "63" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_9744 analysis\n", " 1.27 s in get_analysis_df(\"T1D == 'T1D'\", \"T1D_control == 'T1D_c..., '')\n", " 1.28 s in Loading dataframe for DOID_9744\n", "Matching sources: 13\n", "Excluded 3 sources as single-class\n", "Stats: 10 sources, 8 series, 6 platforms, 416 samples\n", "Loading data and calculating fold change for DOID_9744\n", "Loading data for GSE10586, id = 157\n", "650.84 ms in get_probes(4)\n", " 17.91 s in load_gse( series_id platform_id..., 157, False)\n", " 3.43 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE11907, id = 488\n", "387.05 ms in get_probes(2)\n", "341.26 ms in get_probes(50)\n", " 95.77 s in load_gse( series_id platform_id..., 488, False)\n", " 2.51 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE14368, id = 1122\n", "422.50 ms in get_probes(331)\n", " 5.16 s in load_gse( series_id platform_id..., 1122, False)\n", " 1.51 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE24147, id = 3647\n", "619.02 ms in get_probes(4)\n", " 28.71 s in load_gse( series_id platform_id..., 3647, False)\n", " 4.19 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE29142, id = 4902\n", "455.26 ms in get_probes(937)\n", " 11.17 s in load_gse( series_id platform_id..., 4902, False)\n", " 2.01 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE3447, id = 6176\n", "114.41 ms in get_probes(654)\n", " 2.49 s in load_gse( series_id platform_id..., 6176, False)\n", "379.35 ms in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE55098, id = 10293\n", "616.36 ms in get_probes(4)\n", " 14.53 s in load_gse( series_id platform_id..., 10293, False)\n", " 3.07 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE9006, id = 11628\n", "386.35 ms in get_probes(2)\n", "333.29 ms in get_probes(50)\n", " 43.06 s in load_gse( series_id platform_id..., 11628, False)\n", " 6.98 s in get_gene_fold_change(, False, 0, None)\n", "245.71 s in Load/fold for DOID_9744\n", "Meta-Analyzing DOID_9744\n", "413.09 s in meta analysis of real data for DOID_9744\n", "665.44 ms in meta analysis of permutations for DOID_9744\n", "109.91 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "414.34 s in Meta analysis for DOID_9744\n", "DONE DOID_9744 analysis\n", "661.53 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:9744 type 1 diabetes mellitus\n", "64" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_986 analysis\n", "812.39 ms in get_analysis_df(\"alopecia_areata == 'a..., \"alopecia_areata_contr..., '')\n", "816.68 ms in Loading dataframe for DOID_986\n", "Matching sources: 2\n", "Stats: 2 sources, 2 series, 1 platforms, 17 samples\n", "Loading data and calculating fold change for DOID_986\n", "Loading data for GSE45512, id = 8684\n", "628.17 ms in get_probes(4)\n", " 10.47 s in load_gse( series_id platform_id..., 8684, False)\n", " 2.43 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE58573, id = 10697\n", "621.48 ms in get_probes(4)\n", " 8.49 s in load_gse( series_id platform_id..., 10697, False)\n", " 2.23 s in get_gene_fold_change(, False, 0, None)\n", " 24.13 s in Load/fold for DOID_986\n", "Meta-Analyzing DOID_986\n", "351.41 s in meta analysis of real data for DOID_986\n", "238.83 ms in meta analysis of permutations for DOID_986\n", "108.96 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper I..., Empty DataFrame Column...)\n", "352.32 s in Meta analysis for DOID_986\n", "DONE DOID_986 analysis\n", "377.42 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:986 alopecia areata\n", "65" ] }, { "name": "stderr", "output_type": "stream", "text": [ "Started DOID_9970 analysis\n", "994.06 ms in get_analysis_df(\"obesity == 'obesity'\", \"obesity_control == 'o..., '')\n", "998.34 ms in Loading dataframe for DOID_9970\n", "Matching sources: 43\n", "Excluded 23 sources as single-class\n", "Stats: 20 sources, 14 series, 16 platforms, 561 samples\n", "Loading data and calculating fold change for DOID_9970\n", "Loading data for GSE12050, id = 521\n", "666.94 ms in get_probes(332)\n", " 12.78 s in load_gse( series_id platform_id..., 521, False)\n", " 2.55 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE15524, id = 1461\n", "343.06 ms in get_probes(500)\n", " 7.89 s in load_gse( series_id platform_id..., 1461, False)\n", " 1.59 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE2508, id = 3892\n", "288.37 ms in get_probes(7)\n", "290.41 ms in get_probes(8)\n", "256.84 ms in get_probes(13)\n", "220.59 ms in get_probes(14)\n", "198.40 ms in get_probes(15)\n", "246.18 ms in get_probes(16)\n", " 26.13 s in load_gse( series_id platform_id..., 3892, False)\n", " 4.95 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE2510, id = 3901\n", "385.81 ms in get_probes(2)\n", "332.64 ms in get_probes(50)\n", " 13.67 s in load_gse( series_id platform_id..., 3901, False)\n", " 3.10 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE25401, id = 3977\n", "417.56 ms in get_probes(283)\n", " 16.91 s in load_gse( series_id platform_id..., 3977, False)\n", " 2.81 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE32575, id = 5751\n", "428.92 ms in get_probes(17)\n", " 24.69 s in load_gse( series_id platform_id..., 5751, False)\n", " 2.81 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE44000, id = 8392\n", "508.39 ms in get_probes(53)\n", " 5.55 s in load_gse( series_id platform_id..., 8392, False)\n", " 2.06 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE474, id = 9041\n", "389.45 ms in get_probes(2)\n", " 7.29 s in load_gse( series_id platform_id..., 9041, False)\n", " 1.70 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE48452, id = 9252\n", "408.38 ms in get_probes(953)\n", " 29.44 s in load_gse( series_id platform_id..., 9252, False)\n", " 2.39 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE48521, id = 9261\n", "619.21 ms in get_probes(4)\n", " 14.22 s in load_gse( series_id platform_id..., 9261, False)\n", " 2.74 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE48964, id = 9327\n", "405.64 ms in get_probes(283)\n", " 5.02 s in load_gse( series_id platform_id..., 9327, False)\n", " 1.41 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE55205, id = 10304\n", "511.66 ms in get_probes(674)\n", " 6.59 s in load_gse( series_id platform_id..., 10304, False)\n", " 2.30 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE60403, id = 10836\n", "616.73 ms in get_probes(4)\n", " 13.90 s in load_gse( series_id platform_id..., 10836, False)\n", " 2.74 s in get_gene_fold_change(, False, 0, None)\n", "Loading data for GSE9624, id = 11780\n", "617.37 ms in get_probes(4)\n", " 10.42 s in load_gse( series_id platform_id..., 11780, False)\n", " 2.05 s in get_gene_fold_change(, False, 0, None)\n", "234.78 s in Load/fold for DOID_9970\n", "Meta-Analyzing DOID_9970\n", "456.90 s in meta analysis of real data for DOID_9970\n", " 1.30 s in meta analysis of permutations for DOID_9970\n", "107.05 mks in get_balanced_permutations({'analysis_name': 'DOI..., C H H_lower H_upper \\..., Empty DataFrame Column...)\n", "458.79 s in Meta analysis for DOID_9970\n", "DONE DOID_9970 analysis\n", "694.83 s in perform_analysis({'analysis_name': 'DOI...)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ " DOID:9970 obesity\n" ] } ], "source": [ "errors = list()\n", "\n", "for i, row in query_df.iterrows():\n", " print i, row.slim_id, row.slim_name\n", "\n", " name = row.slim_id.replace(':', '_')\n", " params = easydict.EasyDict(\n", " analysis_name = name,\n", " case_query = row.case_query,\n", " control_query = row.control_query,\n", " modifier_query = '',\n", " min_samples = 3,\n", " )\n", " \n", " directory = os.path.join('data', 'doslim', params.analysis_name)\n", " if not os.path.isdir(directory):\n", " os.mkdir(directory)\n", "\n", " logfile = logging.FileHandler(os.path.join(directory, 'log.txt'))\n", " logfile.setLevel(logging.DEBUG)\n", " starapi.analysis.logger.addHandler(logfile)\n", " try:\n", " sample_df, fold_df, balanced_perm_df, perm_df = starapi.analysis.perform_analysis(params)\n", " for df in fold_df, balanced_perm_df:\n", " if df is not None:\n", " df.reset_index(inplace=True)\n", " \n", " except Exception as e:\n", " sample_df, fold_df, balanced_perm_df, perm_df = None, None, None, None\n", " errors.append({'slim_id': row.slim_id, 'name': name, 'error': e})\n", " print(e)\n", " starapi.analysis.logger.removeHandler(logfile)\n", " \n", " # write files\n", " files = [\n", " (sample_df, 'samples.tsv', open),\n", " (fold_df, 'fold_change.tsv.gz', gzip.open),\n", " (balanced_perm_df, 'balanced_permutation.tsv.gz', gzip.open),\n", " ]\n", " for df, filename, opener in files:\n", " if df is None:\n", " continue\n", " path = os.path.join(directory, filename)\n", " with opener(path, 'wt') as write_file:\n", " df.to_csv(write_file, index=False, sep='\\t', float_format='%.5g')\n" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
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" ], "text/plain": [ "Empty DataFrame\n", "Columns: []\n", "Index: []" ] }, "execution_count": 13, "metadata": {}, "output_type": "execute_result" } ], "source": [ "path = 'data/errors.csv'\n", "if error_df.empty:\n", " if os.path.exists(path):\n", " os.remove(path)\n", "else:\n", " error_df = pandas.DataFrame(errors)\n", " error_df = query_df.merge(error_df)\n", " error_df.to_csv(path, index=False)\n", "\n", "error_df" ] } ], "metadata": { "kernelspec": { "display_name": "Python 2 - stargeo", "language": "python", "name": "stargeo" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 2 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython2", "version": "2.7.10" } }, "nbformat": 4, "nbformat_minor": 0 }