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    "# Pre-processing scripts\n",
    "This notebook will explain what pre-processing was done to the data, which includes: \n",
    "* combining primary data into simple tsv format\n",
    "* calculating log2 ratios\n",
    "* averaging duplicate cell line measurements\n",
    "* making a CCLE-comparable version of the PTM data (e.g. keep only 37 cell lines from CCLE)\n",
    "\n",
    "### Make CCLE-comparable version of PTM data \n",
    "The script \n",
    "\n",
    "`make_CCLE_comparable_matrix.py` \n",
    "\n",
    "combines all PTM data types (phosphorylation, methylation, acetylation) into a single tsv file. Then it averages duplicate measurements of cell lines (some cell lines were measured in two different plexes). Finally, it saves a tsv file with only the 37 cell lines that were found in the CCLE data. \n",
    "\n",
    "The final combined PTM data with comparable cell lines is saved in \n",
    "`lung_cellline_3_1_16/lung_cl_all_ptm/all_ptm_ratios_CCLE_cl.tsv`\n",
    "\n",
    "\n",
    "### Pre-calculate Normalizations and Similarity Matrices\n"
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