mirrorCheck: an R package facilitating informed use of DESeq2’s lfcShrink() function for differential gene expression analysis of clinical samples

Abstract

Motivation: The sophisticated lfcShrink() function implemented in the DESeq2 package for differential gene expression analysis aims to reduce noise from low read count and/or highly variable genes in bulk RNA-sequencing data, thus circumventing the need for arbitrary filtering thresholds. However, difficulties can arise when analysing clinical data with multiple biologically-relevant groupings. In particular, changing the reference group can dramatically alter the ranking of differentially expressed genes, instead of merely ‘mirroring’ the up- and down-regulated genes in reciprocal comparisons. Results: Here, we present mirrorCheck, an R package to automate methodical lfcShrink() usage and d..