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Old 01-21-2012, 06:52 AM   #6
Simon Anders
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Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994
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The good thing about the false discovery rate (FDR) is that it has a clear, easily understandable, meaning. If you cut at an FDR value of 0.1 (10%), your list of significant hits has (in expectation) at most 10% false positives. So, if you get 60 genes with FDR-adjusted p value below 10%, this list will contain around 6 false ones.

The reason that there is no consensus on which FDR level to chose is that it is not asked too much to make an informed case-by-case decision what FDR might be acceptable for a given experiment, depending on the kind of conclusions one whishes to draw.

And just as a reminder: Don't even think about thresholding the raw p values in genomic experiments. This is nearly always nonsense, and I wish editors would make it a rule to simply reject papers doing that immediately instead of waiting for the referees to spot it.
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