# [R] Adjusting p values of a matrix

January Weiner january.weiner at mpiib-berlin.mpg.de
Tue Apr 5 12:02:35 CEST 2011

> 1. This is not an R question, AFAICS.

I am afraid I was not clear enough. I am wondering how to best correct
p values that are stored in a matrix, or, in more general: how to
apply a function that takes a vector as an argument to the upper right
(or, equivalently, lower left) half of a matrix, excluding the
diagonal. for... in loop is a trivial, but slow and not elegant
solution.

Naturally, what correction should I use in case of tests which clearly
are not independent is another matter, and I agree on that with you.

Best regards,

January

>
> 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
>>
>> ______________________________________________
>> R-help at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>
>
> --
> "Men by nature long to get on to the ultimate truths, and will often
> be impatient with elementary studies or fight shy of them. If it were
> possible to reach the ultimate truths without the elementary studies
> usually prefixed to them, these would not be preparatory studies but
> superfluous diversions."
>
> -- Maimonides (1135-1204)
>
> Bert Gunter
> Genentech Nonclinical Biostatistics
>

--
-------- 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