Peter Degen

Discussion We have comprehensively analyzed the replicability and reliability of RNA-Seq differential expression results obtained from small cohorts. Compared to recent work by Cui et al. [14], we used a wider variety of data sets, considered multiple tools for the analysis, characterized fold change thresholding strategies, and evaluated the impact of low replicability on downstream enrichment analysis (see Table B in S1 Text for a detailed comparison of the methodology used).

Abstract The high-dimensional and heterogeneous nature of transcriptomics data from RNA sequencing (RNA-Seq) experiments poses a challenge to routine downstream analysis steps, such as differential expression analysis and enrichment analysis. Additionally, due to practical and financial constraints, RNA-Seq experiments are often limited to a small number of biological replicates; three replicates is a commonly employed minimum cohort size.