Table 1.
A comparison of common statistical methods for RNA-Seq differential gene expression analysis
| 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] |