[Rd] p.adjust(<NA>s), was "Re: [BioC] limma and p-values"
maechler at stat.math.ethz.ch
Mon Jan 17 21:45:40 CET 2005
>>>>> "GS" == Gordon Smyth <smyth at wehi.edu.au>
>>>>> on Sun, 16 Jan 2005 19:44:26 +1100 writes:
GS> The new committed version of p.adjust() contains some
GS>  0.05 0.50
GS> No adjustment!
yes, but that's still better than what the current version of
R 2.0.1 does, namely to give NA NA + two warnings ..
GS> I can't see how the new treatment of NAs can be
GS> justified. One needs to distinguish between NAs which
GS> represent missing p-values and NAs which represent
GS> unknown p-values. In virtually all applications giving
GS> rise to NAs, the NAs represent missing p-values which
GS> could not be computed because of missing data. In such
GS> cases, the observed p-values should definitely be
GS> adjusted as if the NAs weren't there, because NAs
GS> represent p-values which genuinely don't exist.
hmm, "definitely" being a bit strong. One could argue that
ooonoe should use multiple imputation of the underlying missing
data, or .. other scenarios.
I'll reply to your other, later, more detailed message
separately and take the liberty to drop the other points here...
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