A bit more about TMM

This blog is short, but I still want to post it to keep the writing mood. It is barely a paragraph though…

  • /A scaling normalisation method for differential expression analysis of RNA-Seq data/, Genome Biology, 2010. I spent some more time on TMM, but I would not say I fully get the normalisation procedures. However, the basic assumption is that most of genes in samples are not differential expressed genes, so that it tries finding a scaling factor to minimise the log-fold changes of genes between samples. TMM stands for Trimmed Mean of M-values. The M values are just the log-folds of genes between samples, and the Trimmed Mean simply means that some M values (e.g. 30% of the M on two sides) are removed before calculating their mean.

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