[BioC] p-value adjustment

[Wenbin Liu]

Thanks Matthew and Gordon for your comments.  

Wenbin


--- Matthew  Hannah <Hannah at mpimp-golm.mpg.de> wrote:
> One thing to add on this point that might be of
> interest is that an
> initial look at p.adjust
> p.adjust(p, method = p.adjust.methods, n =
> length(p))
> would suggest that including NAs would result in
> more conservative
> correction as n > # of p-values, but it doesn't (at
> least for fdr) as
> the NAs are ordered below the minimum p-value from
> your vector in the
> calculation. So if you fdr correct with the NAs
> present then you get
> more significant p-values than you should and the
> results are
> meaningless - and there's no error message.
> 
> Obviously, the nice work by the developers will
> correct this.
> 
> >>Wenbin Liu wnbnl at yahoo.com
> >>Wed Mar 23 23:51:28 CET 2005
> >>
> >>Dear list,
> >>
> >>I'm puzzled by the R function p.adjust with NA
> values
> >>in the first argument. The adjustment gives
> different
> >>result with and without the NAs.
> >
> >Please refer to the extensive recent discussion on
> this topic on the 
> >R-devel mailing list.
> >
> >>  The question then is,
> >>which approach should one take: with or without
> NAs in
> >>the first argument?
> >
> >The limma package functions remove NAs before using
> p.adjust(), and I 
> >believe this is virtually always correct in the
> microarray context.
> >
> >Gordon
> >
> >>Thanks a lot!
> >>
> >>Wenbin
> 
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