bio-experimental-design-multiple-testing

Version Compatibility

Reference examples tested with: R stats (base), statsmodels 0.14+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

Multiple Testing Correction

"Correct p-values for multiple testing" → Adjust raw p-values from thousands of simultaneous tests to control false discovery rate or family-wise error rate.

• R: p.adjust(pvalues, method = 'BH'), qvalue::qvalue()
• Python: statsmodels.stats.multitest.multipletests()

The Problem

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

Common Methods

Bonferroni (Most Conservative)

# Strict family-wise error rate control
p_adj <- p.adjust(pvalues, method = 'bonferroni')
# Threshold: alpha / n_tests
# Use for: small gene sets, confirmatory studies

Benjamini-Hochberg FDR (Standard)

# Controls false discovery rate
p_adj <- p.adjust(pvalues, method = 'BH')
# Most common for genomics
# FDR 0.05 = expect 5% of significant results to be false

q-value (Recommended for Large-Scale)

Goal: Estimate the false discovery rate for each gene in a genome-wide test while maximizing detection power by estimating the proportion of true nulls.

Approach: Fit the q-value model to the p-value distribution, which estimates pi0 (fraction of true null hypotheses) and converts each p-value to a q-value representing the minimum FDR at which that gene would be called significant.

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

# q-value directly estimates FDR for each gene
# More powerful than BH when many true positives exist