I am looking into differential expression analyses of RNA Seq data. Having worked with arrays previously, I am quite used to the FDR to adjust for multiple testing. Thus far, I have always used 0.05 as the cutoff.
Looking into different ways to analyze the data, especially the DESeq2 package that several of you recommended, it seems to me that an adjusted p-value of 0.1 is the norm now.
I guess the answer is probably "it depends", but I can foresee reviewers questioning this...
What do you think?
Many thanks for your input!