{
  "engine": {
    "R": "R version 4.4.3 (2025-02-28)",
    "affy": "1.84.0",
    "limma": "3.62.1",
    "cdf": "2.18.0"
  },
  "workflow": "ReadAffy -> affy::rma -> one representative probeset per Arabidopsis locus by label-independent overall variance -> limma tissue-specific model (~ condition + plate) -> eBayes",
  "samples": 36,
  "probesets": 22810,
  "loci": 22591,
  "tissue_summary": [
    {
      "tissue": "whole plant",
      "genes_tested": 22591,
      "fdr_005": 0,
      "p001": 417,
      "_row": "whole plant"
    },
    {
      "tissue": "shoot",
      "genes_tested": 22591,
      "fdr_005": 47,
      "p001": 821,
      "_row": "shoot"
    },
    {
      "tissue": "hypocotyl",
      "genes_tested": 22591,
      "fdr_005": 31,
      "p001": 824,
      "_row": "hypocotyl"
    },
    {
      "tissue": "root",
      "genes_tested": 22591,
      "fdr_005": 351,
      "p001": 1004,
      "_row": "root"
    }
  ],
  "concordance": [
    {
      "tissue": "whole plant",
      "shared_loci": 22591,
      "effect_spearman": 0.99445842,
      "top300_overlap": 255,
      "top300_same_direction": 1,
      "bioc_fdr_005": 0,
      "python_fdr_005": 0,
      "_row": "whole plant"
    },
    {
      "tissue": "shoot",
      "shared_loci": 22591,
      "effect_spearman": 0.99593706,
      "top300_overlap": 256,
      "top300_same_direction": 1,
      "bioc_fdr_005": 47,
      "python_fdr_005": 30,
      "_row": "shoot"
    },
    {
      "tissue": "hypocotyl",
      "shared_loci": 22591,
      "effect_spearman": 0.99600676,
      "top300_overlap": 257,
      "top300_same_direction": 1,
      "bioc_fdr_005": 31,
      "python_fdr_005": 18,
      "_row": "hypocotyl"
    },
    {
      "tissue": "root",
      "shared_loci": 22591,
      "effect_spearman": 0.99620276,
      "top300_overlap": 284,
      "top300_same_direction": 1,
      "bioc_fdr_005": 351,
      "python_fdr_005": 286,
      "_row": "root"
    }
  ],
  "interpretation": "Independent implementation check. It tests computational reproducibility, not biological validation."
}