Abstract
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.
Here we present mirrorCheck, an R package to automate methodical lfcShrink() usage and data visualisation for quality control and data-driven decision-making during analysis.
The source code, including documentation, is available on github at https://github.com/kescull/mirrorCheck.
Accepted manuscripts
