Table 1 A comparison of common statistical methods for RNA-Seq differential gene expression analysis
From: Statistical methods for identifying differentially expressed genes in RNA-Seq experiments
Method | Underlying distribution | Recommended with biological replicates | Multi-group comparison | R/Bioconductor package | Reference |
|---|---|---|---|---|---|
Fisher’s exact Test | Poisson | No | No | No | [27] |
Likelihood ratio test | Poisson | No | Yes | No | [21] |
edgeR | Negative Binomial | Yes | Yes | Yes | [28] |
DESeq | Negative Binomial | Yes | No | Yes | [15] |
baySeq | Negative Binomial | Yes | Yes | Yes | [17] |
BBSeq | Beta-Binomial | Yes | No | Yes | [29] |
Two-stage poisson model | Poisson | Yes | Yes | No | [30] |