mirrorCheck: an R package facilitating informed use of DESeq2's lfcShrink() function for differential gene expression analysis of clinical samples
- Author(s)
- Scull, KE; Behrouzfar, K; Brasacchio, D; Lam, EYN; Chandrananda, D; Yeh, P;
- Details
- Publication Year 2025,Volume 5,Issue #1,Page vbaf070
- Journal Title
- Bioinformatics Advances
- Publication Type
- Research article
- 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 data visualization for quality control and data-driven decision-making during analysis. AVAILABILITY AND IMPLEMENTATION: The source code, including documentation, is available on github at https://github.com/kescull/mirrorCheck.
- Publisher
- Oxford University Press
- Department(s)
- Laboratory Research
- Publisher's Version
- https://doi.org/10.1093/bioadv/vbaf070
- Open Access at Publisher's Site
https://doi.org/10.1093/bioadv/vbaf070- Terms of Use/Rights Notice
- Refer to copyright notice on published article.
Creation Date: 2026-01-15 11:50:41
Last Modified: 2026-01-15 11:51:01