Hi, I have a RNAseq data and I generally perform the DESeq2 analysis setting "Independent filtering=T". Is it sensible to filter the out transcripts/genes which has raw counts < 20 and then apply "Independent filtering=T"? Kindly guide me.
Thanks in advance
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EVR
There's not much of a point in prefiltering if you're going to independently filter anyway.
The only advantage I see is to end up with a smaller table and save a bit of memory from the start. This however would probably not be noticeable for most analysis on a decent computer.
Indeed, if someone had enough samples to worry about memory then I expect the overall performance of DESeq2 would be abysmal (this is a case for limma, then).
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