Still somewhat new to handling transcriptomic data, and have a newbie question.
I'm just trying to convert some RNA-Seq count data to TPM for the purpose of presenting qualitative comparisons about relative expression of various genes in a single cell type/condition. I'm aware that for comparisons between conditions TPM is not optimal.
I have a matrix of both raw counts for each gene/condition, and corrected counts generated by DESeq2.
My question is, could I use the DESeq2 corrected count data for the TPM conversion? My reason for doing this is that I have heard that DESeq2's normalisation method is more robust when correcting for library size and RNA composition than the TPM method. Obviously since TPM normalises after adjusting for gene length, it will still change the relative quantities slightly, but from a slightly better starting point?
Just wanted to check I'm not missing some obvious reason why this would be worse than just doing the TPM conversion on the raw count matrix?