> 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.wei...@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@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> 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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
