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bio-experimental-design-multiple-testing

Maintainer FreedomIntelligence · Last updated April 1, 2026

Multiple testing correction: Bonferroni, BH/FDR, q-values.

OpenClawNanoClawAnalysisReproductionbio-experimental-design-multiple-testing🧠 bioos extended suitebioos extended bioinformatics suitemultiple

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-experimental-design-multiple-testing

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

p_adj <- p.adjust(pvalues, method = 'bonferroni').
p_adj <- p.adjust(pvalues, method = 'BH').

Source Doc

Excerpt From SKILL.md

The Problem

Testing 20,000 genes at p < 0.05 yields ~1,000 false positives by chance. Correction is essential.

q-value (Recommended for Large-Scale)

library(qvalue)
qobj <- qvalue(pvalues)
qvalues <- qobj$qvalues
pi0 <- qobj$pi0  # Estimated proportion of true nulls

## Method Selection Guide

| Scenario | Recommended Method | Threshold |
|----------|-------------------|-----------|
| Genome-wide DE | BH or q-value | FDR < 0.05 |
| Candidate genes | Bonferroni | p < 0.05/n |
| Exploratory | BH | FDR < 0.10 |
| Validation study | Bonferroni | p < 0.05/n |
| GWAS | Bonferroni | p < 5e-8 |

Use cases

Use bio-experimental-design-multiple-testing for genomics and bioinformatics workflows.
Apply bio-experimental-design-multiple-testing to sequencing, variant, or omics analysis tasks.