Hello there, I know you are not recommending to perform t-test when doing rna-seq but I really need to know how to perform the latter because the core facility who analysed my samples did this and apparently don't want to disclose the code used at this stage. The reason why I am so keen is that, when validating a few genes via qPCR here there is indeed a significant change for the genes obtained with this approach (t-test). Those genes didn't show up with the normal approach.
I guess they are using tximport as scaledTPM and then counts are used outside, R in excel to perform a t-test? Is that possible?