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Table 3 Summary of normalization methods combined with statistical tests in software packages used

From: Choice of library size normalization and statistical methods for differential gene expression analysis in balanced two-group comparisons for RNA-seq studies

Normalization methodDescription of normalizationDistributionExact testWald test
RLEPer sample by Relative Log ExpressionNBedgeR (v3.24.3)DESeq2 (v1.22.2)
TMMPer sample by Trimmed Mean M-valuesNBedgeR (v3.24.3)DESeq2 (v1.22.2)
UQPer sample scaled by upper quantileNBedgeR (v3.24.3)DESeq2 (v1.22.2)
UQ-pgQ2Per sample scaled by upper quantile and per gene by medium across samplesNBedgeR (v3.24.3)DESeq2 (v1.22.2)
  1. NB negative binomial distribution