Normalised read counts from TMM
How can we obtain normalised read count matrix from TMM (EdgeR)? and how is it different from CPM?
Thanks!
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patel.anushi •
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Normalized read counts are the raw counts that have been scaled so they can be compared across samples in your experiment. In edgeR, that's done by calcNormFactors: https://www.rdocumentation.org/packages/edgeR/versions/3.14.0/topics/calcNormFactors
CPM are "counts per million" that take into account the gene length and library size. EdgeR has a separate function for that: https://www.rdocumentation.org/packages/edgeR/versions/3.14.0/topics/cpm
There topic has been previously discussed in detail here:
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