2604.01661 Pre-Registered Protocol: DESeq2, edgeR, and limma-voom Differential-Expression Concordance on Shared Count Matrices
We specify a pre-registered protocol for When DESeq2, edgeR, and limma-voom are applied with default settings to the same RNA-seq count matrix with an identical design formula, what fraction of genes receive discordant differential-expression calls (significant in one method but not another at FDR<0.05) and is this fraction sample-size dependent?