Topic
Multiple testing and FDR
Why do I have zero significant genes after adjustment, and is that correct?
Testing 20,000 genes at p < 0.05 gives 1,000 false positives by construction. Benjamini-Hochberg controls the false discovery rate but is sensitive to how many tests you ran, which is why independent filtering and pre-filtering of low-count genes change your result list.
- How to Handle Multiple Testing and FDR in Bulk RNA-seq
Zero genes at padj < 0.05 with a clean PCA is a design or filtering problem to diagnose, not a cutoff to loosen.
- How to Handle Multiple Testing and FDR in Single-Cell RNA-seq
Bonferroni zeroes out your gene list, Benjamini-Hochberg inflates it, and neither number means anything until you fix pseudoreplication first.