{
  "scope": "Real public airway processed gene counts; no FASTQ mapping, original-paper replication or functional validation",
  "data": {
    "package": "airway",
    "geo": "GSE52778",
    "input_genes": 63677,
    "samples": 8,
    "paired_cell_lines": 4,
    "upstream_reference": "GRCh37 / Ensembl release 75 as described in airway vignette",
    "prefilter": "rowSums(raw_counts) >= 10",
    "retained_genes": 22369
  },
  "model": {
    "design": "~ cell + dex",
    "contrast": "trt versus untrt",
    "alpha": 0.05,
    "design_rank": 5,
    "residual_df": 3,
    "shrinkage": "apeglm; original Wald P and padj retained; posterior SD is not original Wald SE",
    "threshold_test": "H0: abs(log2FC) <= 1, greaterAbs"
  },
  "results": {
    "significant": 4030,
    "up": 2208,
    "down": 1822,
    "status_counts": {
      "tested": 17165,
      "independent_filter": 5204,
      "pvalue_NA_review_Cooks_or_other": 0
    },
    "no_independent_filter_significant": 3820,
    "threshold1_significant": 243,
    "independent_filter_baseMean_threshold": 6.1363644452,
    "pca_percent_variance": [0.47842864474, 0.23383404452]
  },
  "checks": {
    "shuffled_metadata_aligned_by_ID": true,
    "paired_design_full_rank": true,
    "reverse_contrast_negates_LFC_preserves_P": true,
    "unfiltered_padj_matches_BH": true,
    "shrinkage_preserves_Wald_P_and_padj": true
  },
  "versions": {
    "R": "4.4.3",
    "airway": "1.26.0",
    "DESeq2": "1.46.0",
    "apeglm": "1.28.0",
    "jsonlite": "2.0.0"
  }
}