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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]