Table 3 Summary of normalization methods combined with statistical tests in software packages used
Normalization method | Description of normalization | Distribution | Exact test | Wald test |
|---|---|---|---|---|
RLE | Per sample by Relative Log Expression | NB | edgeR (v3.24.3) | DESeq2 (v1.22.2) |
TMM | Per sample by Trimmed Mean M-values | NB | edgeR (v3.24.3) | DESeq2 (v1.22.2) |
UQ | Per sample scaled by upper quantile | NB | edgeR (v3.24.3) | DESeq2 (v1.22.2) |
UQ-pgQ2 | Per sample scaled by upper quantile and per gene by medium across samples | NB | edgeR (v3.24.3) | DESeq2 (v1.22.2) |