How can I get the normalized counts matrix after doing TMM normalization using edgeR

Question

[debitboro]

Hi biostars community,

How can I get the normalized counts matrix after doing TMM normalization using edgeR ? I saw a response in an older post that we can get this matrix by using cpm() function of edgeR package, but I think the CPM normalization method is different from the TMM method. is that right ?

thanks all

Answer 1

[le2336]

See this discussion: https://support.bioconductor.org/p/77193