I have Salmon output files from 9 samples - 3 biological replicates from 3 different treatment groups.
I need to perform DE analysis on these Salmon output files.
Firstly, from what I understand, it is uncouth to perform DE analysis on TPM values - I still don't understand why, since the values are normalized for library depth and transcript length, aren't these the best values to perform DE analysis on?
Secondly, is there a tutorial for importing Salmon files using tximport package into R that's written in layman English. I tried the Galaxy-based DEseq2 and picked the TPM option, but was informed by one of the moderators that the online tool has never worked properly with TPM values. So, I am left at the mercy of R, which I am not too friendly with.
Any help would be much appreciated.
Any recommendation on good DESeq2 tutorials in R would be much appreciated.