I am having some doubts about filtering low counts. I already read and read ... papers, questions in forums and i still have the same issue. I know that deseq2 has the independent filtering in the results() however after trying different alpha thresholds my results differs on number of DEGs ok but not quite the genes that my client looking for :) i know, i know this is the result, if dont appear its because its not suppose too! However, if i apply the method 2 of filtering with noiseq package i got the genes that client want! This method was applied before the normalization which removed alot of genes... My question is can i use the noiseq filter or just give the results that i got only with independent filter from deseq2?
Thanks in advance.