[R] Adjusting p values of a matrix

Bert Gunter gunter.berton at gene.com
Mon Apr 4 17:54:32 CEST 2011

1. This is not an R question, AFAICS.

2. Sounds like a research topic.  I don't think there's a meaningful
simple answer. I suspect it strongly depends on the model and context.

-- Bert

On Mon, Apr 4, 2011 at 8:02 AM, January Weiner
<january.weiner at mpiib-berlin.mpg.de> wrote:
> Dear all,
> I have an n x n matrix of p-values. The matrix is symmetrical, as it
> describes the "each against each" p values of correlation
> coefficients.
> How can I best correct the p values of the matrix? Notably, the total
> number of the tests performed is n(n-1)/2, since I do not test the
> correlation of each variable with itself. That means, I only want to
> correct one half of the matrix, not including the diagonal. Therefore,
> simply writing
> pmat <- p.adjust( pmat, method= "fdr" )
> # where pmat is an n x n matrix
> ...doesn't cut it.
> Of course, I can turn the matrix in to a three column data frame with
> n(n-1)/2 rows, but that is slow and not elegant.
> regards,
> j.
> --
> -------- Dr. January Weiner 3 --------------------------------------
> Max Planck Institute for Infection Biology
> Charitéplatz 1
> D-10117 Berlin, Germany
> Web   : www.mpiib-berlin.mpg.de
> Tel     : +49-30-28460514
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"Men by nature long to get on to the ultimate truths, and will often
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-- Maimonides (1135-1204)

Bert Gunter
Genentech Nonclinical Biostatistics

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