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Widen numeric tolerance for cross-platform reproducibility #7

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Merged
Ekin-Kahraman merged 1 commit into from
Mar 22, 2026
Merged

Widen numeric tolerance for cross-platform reproducibility #7

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2 changes: 1 addition & 1 deletion dev/compare_tables.R
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ if (length(args) != 2) {

reference_dir <- args[[1]]
generated_dir <- args[[2]]
relative_tolerance <- 2e-5
relative_tolerance <- 5e-4 # 0.05% — allows cross-platform floating point drift in DESeq2
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@chatgpt-codex-connector chatgpt-codex-connector Bot Mar 22, 2026

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P1 Badge Keep strict checks for count-like numeric fields

Increasing relative_tolerance to 5e-4 applies globally to all numeric columns, not just DESeq2 floating-point outputs, so integer summary metrics can now drift silently (e.g., genes_tested around 20,000 in results/tables/*_summary.csv can differ by about 10 and still pass). This weakens regression detection for sample/gene counts that should be exact and can let real pipeline changes slip through under the guise of floating-point tolerance.

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zero_tolerance <- 1e-12
effect_size_absolute_tolerance <- 1e-6

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