I was looking through the vignette for tximport, and it has recommendations for how to import data for downstream analysis in edgeR, DESeq2 and limma-voom, but it does not mention the lesser-used limma-trend. The edgeR method stores the length corrections in y$offset, but the voom() function does not use the y$offset so tximport recommends importing either "scaledTPM" or "lengthScaledTPM". The limmaUsersGuide() suggests doing
logCPM <- cpm(y, log = TRUE, prior.count = 3). I thought that since cpm() is an edgeR function it would use the y$offset, but looking at the code of cpm.DGEList, it doesn't use y$offset either. So am I correct in assuming that I should use the tximport method for limma-voom, but then should use cpm() instead of voom()?