count TMM-trimmed mean of M-values corrected count TMM TMM "calcNormFactors"(object, method=c("TMM","RLE","upperquartile","none"), refColumn=NULL, logratioTrim=.3, sumTrim=0.05, doWeighting=TRUE, Acutoff=-1e10, p=0.75, ...) from: https://www.rdocumentation.org/packages/edgeR/versions/3.14.0/topics/calcNormFactors https://doi.org/10.1186/gb-2010-11-3-r25 and https://doi.org/10.1093/bioinformatics/btp616 and https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html Philippe Rocca-Serra TMM or Trimmed Mean of M-Values is a measurement datum which is the output of the TMM normalization procedure for RNA-Seq data proposed by Robinson and Oshlack (2010). A scaling normalization method for differential expression analysis of RNA-seq data. The TMM procedure is doubly trimmed, by log-fold-changes (sample k relative to sample r for gene g) and by absolute intensity (A g ). It was first release as part of the R package edgeR, 10.1093/bioinformatics/btp616 Recommended use: -TMM measure is suited for gene count comparisons within a sample or between samples of the same sample group. -TMM measure is suited for Differential Expression analysis. ready for release