Hi, I have a question about the results of DESeq2. Usually, I use q-value<=0.05 and |FC|>2 as the criteria to screen differentially expressed genes. If I want to identify genes with similar expression under different conditions, which criteria should I use? I was thinking of only using q-value>0.05. But there are also some genes with |FC|~1 and q-value<=0.05. Thank you very much!

See the vignette and the paper, we have a way to specify that the alternative hypothesis should be LFC less than X in absolute value.