My first question here. I'll make it as short and concise as possible. Please correct me if I am wrong (which I very well might be).
I would like to obtain between sample normalized, within sample normalized gene expression values, e.g. size factor adjusted TPM values. I have quantified my RNA-seq experiment using Salmon and imported the results with tximport to do the differential analysis with DESeq2. Tximport allows the use of the TPM values from Salmon to do the differential analysis, but entails a transformation of said values to either scaledTPM or lengthScaledTPM values.
As I understand it, the scaledTPM values are the between-sample normalized TPM values multiplied by the library size in millions. So something like "transcripts pr sample", which is not really what I want.
My question is, would it be possible to somehow output between sample normalized TPM values for each gene or is this somehow violation a principle I am overlooking?
Could I just divide the the TPMs from Salmon with the sizeFactors obtained from DESeq2?