TMM Normalisation

Excerpts from "NormalizationAndDifferentialExpression"

tmm <- calcNormFactors(geneCounts.dgelist)

# equation from the edgeR documentation for estimating normalized absolute expression from their scaling factors
tmmScaleFactors <- geneCounts.dgelist$samples$lib.size * tmm$samples$norm.factors
tmmExp <- round(t(t(tmm$counts)/tmmScaleFactors) * mean(tmmScaleFactors))

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Excerpts from "Question: After Getting Normalization Factor Via Edger, What To Do For Normalization?"

The TMM counts are: count / (library size * normalization factor)

Then multiply that by a million to get CPM.

Not count / normalization factor

And DESeq doesn't just do a simple division by library size. It takes the median of the ratio of the count to the geometric mean of the expression values as the scaling factor for each library.