Adjusting p values of a matrix
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 Charit?platz 1 D-10117 Berlin, Germany Web?? : www.mpiib-berlin.mpg.de Tel? ?? : +49-30-28460514
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-------- Dr. January Weiner 3 -------------------------------------- Max Planck Institute for Infection Biology Charit?platz 1 D-10117 Berlin, Germany Web?? : www.mpiib-berlin.mpg.de Tel? ?? : +49-30-28460514