Hi I am using Partek to analyze RNA-seq data, Partek has a median normalization step before Deseq2, which works fine. I understand Deseq2 takes raw data, but Partek has separated the normalization step recently (previously it normalization used to be part of Deseq2 in Partek).
While playing with the various normalizations, I have noticed that if I use TMM normalization followed by Deseq2, I get much better results. I know TMM is for EdgeR but unfortunately Partek does not have EdgeR.
Is there anyway, one can get away with using TMM normalized input for a modified Deseq2, which has its median normalization disabled?