I did all my RNA-seq analysis for 500 patients with the EdgeR workflow as described in the manual. Now I read an article (F1000 research) where they state that EdgeR is mostly preferred in low-count situations, where limma-voom is recommended in large scale datasets. I thought using EdgeR was fine for my experiment, but this article has me worried. Would limma-voom be preferred in my case or is EdgeR equally fine? Maybe good to know, I have no problems with computational times when using EdgeR.
Many thanks in advance!