I am currently using the edgeR package for RNASeq analysis, however, I have a bit of a problem. In the current dataset that I am working on, I noticed that following calculation of the tagwise dispersion that the FDR for all of the genes is 1. However, this doesn't occur after estimating the common and trended dispersion. Any feedback on as to why this may be occurring is greatly appreciated. I am using edgeR version 3.22.5. Many thanks, Lisa.
Thank you so much for your feedback. And yes you are correct, I am using LRT methods. I hadn't given the quasi-likelihood method a try but I will now do so.