[Rd] p.adjust(<NA>s), was "Re: [BioC] limma and p-values"
Peter Dalgaard
p.dalgaard at biostat.ku.dk
Tue Jan 18 13:57:56 CET 2005
Martin Maechler <maechler at stat.math.ethz.ch> writes:
> MM> I agree that I don't see a good reason to allow specifying 'n'
> MM> as argument unless e.g. for "bonferroni".
> MM> What do other think ?
>
> no reaction yet.
>
> I've thought a bit more in the mean time:
> Assume someone has 100000 P values and knows that he
> only want to adjust the smallest ones.
> Then, only passing the ones to adjust and setting 'n = 100000'
> can be useful and will certainly work for "bonferroni" but
> I think it can't work in general for any other method.
>
> In sum, I still tend to agree that the argument 'n' should be
> dropped -- but maybe with "deprecation" -- i.e. still allow it
> for 2.1.x giving a deprecation warning.
There's another case to consider, namely when you get the same tests
multiple times. Think SAS, for instance; when it compares groups you
get every comparison twice: I vs III as well as III vs I, so you need
a way to say that there are really only k * (k - 1) / 2 tests. Then
again, this probably only works for "bonferroni", and R's
pairwise.t.test() evades this by extracting the lower.tri before
adjustment.
--
O__ ---- Peter Dalgaard Blegdamsvej 3
c/ /'_ --- Dept. of Biostatistics 2200 Cph. N
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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