Sorry I know that this question has been asked several times, but unfortunately I haven't been able to find the right answer, or didn't understand.
I'm trying to get TMM normalized counts thanks to edgeR.
I understand that I have to compute normalization factors :
dgList <- calcNormFactors(dgList, method="TMM")
which gives me a normalization factor for all samples :
head(dgList$samples) group lib.size norm.factors S1 1 21087314 0.9654794 S2 1 16542810 1.1589117 S3 1 18875473 0.8763291 S4 1 15865414 1.0864038 S5 1 19179795 1.0488230 S6 1 15063992 1.0707007
But at this step I don't know what to do to get a matrix of normalized TMM counts.
I know that I can get CPM normalized counts thanks to :
But CPM and TMM are not the same, right ?
Thanks in advance for any of your input on this topic.