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7.1 years ago
patel.anushi
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0
How can we obtain normalised read count matrix from TMM (EdgeR)? and how is it different from CPM?
Thanks!
How can we obtain normalised read count matrix from TMM (EdgeR)? and how is it different from CPM?
Thanks!
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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