mirrorCheck: an R package facilitating informed use of DESeq2's lfcShrink() function for differential gene expression...

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Differential gene expression analysis using DESeq2's lfcShrink() function is crucial for RNA-sequencing data.
• The function aims to reduce noise from low read counts and highly variable genes without arbitrary filtering.
• Clinical data with multiple biological groupings can present challenges, particularly when altering reference groups.

Purpose of the Study:

• To address the issue of altered gene expression rankings when changing reference groups in DESeq2.
• To provide a tool for methodical lfcShrink() usage and data visualization for quality control.
• To aid in data-driven decision-making during differential gene expression analysis.

Main Methods:

• Development of an R package named mirrorCheck.
• Automation of lfcShrink() function application and associated data visualization.
• Implementation of quality control measures for differential gene expression analysis.

Main Results:

• The mirrorCheck package automates the quality control process for lfcShrink() in DESeq2.
• It facilitates methodical usage and visualization, improving data-driven decision-making.
• The package helps identify and manage potential alterations in gene expression rankings due to reference group changes.

Conclusions:

• mirrorCheck provides a robust solution for quality control in differential gene expression analysis with DESeq2.
• The package enhances the reliability of results when analyzing complex clinical datasets with multiple groupings.
• It ensures more consistent and interpretable differential gene expression findings.