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Old 01-27-2014, 10:15 AM   #19
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Originally Posted by dpryan View Post
@rskr: Given that this is in the context of DESeq2 (I realize that the thread is titled with edgeR...), low-count genes are automatically dropped and power maximized (I have to admit that it's handy to not have to do this myself anymore). So, the low-coverage genes screwing the p-values critique doesn't apply.
Low coverage genes can still be significant, just not at the same rate as the higher coverage genes, though it may be possible to filter out certain genes which have zero chance of being significant, however the power to tell depends on the proportion as well as the coverage, so as I said FDR isn't so important.
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