Hello,
Quick question regarding independent filtering and prefiltering. In my differential expression analysis pipeline, I filter out genes based on a quantile threshold prior to running DESeq2. My question is, since I already did this prefiltering step prior to running DESeq2, should I turn the option for independent filtering off when I run the DEseq() command, or should I keep it on? Will it skew results if I run the independent filter on already pre-filtered data? Please let me know.
Leave it on. Just follow the manual. It includes optional prefiltering and does not recommend to turn off IF. Don't reinvent the wheel. Follow the expert suggestions in the vignette.