Full_Name: Ludo Pagie Version: 2.8.1 OS: linux Submission from: (NULL) (194.171.7.39)
p.adjust in stats seems to have a bug in handling n>length(p) for (at least) the methods 'holm' and 'hochberg'. For method 'holm' the relevant code: i <- 1:n o <- order(p) ro <- order(o) pmin(1, cummax((n - i + 1) * p[o]))[ro] where p is the supplied vector of pvalues and n is the supplied number of comparisons. If n>length(p) p.adjust() gives a warning: Warning message: In (n - i + 1) * p[o] : longer object length is not a multiple of shorter object length to me it seems that instead of 'i <- 1:n', 'i <- 1:length(p)' is required. Similar cases seem to be true for 'hochberg' and possibly other methods. (I tried checking whether this bug has been reported but the website broke on me. appologies if the bug is known already) Best, Ludo Netherlands Cancer Institute Gene Regulation (B4) van Steensel Group Plesmanlaan 121 1066 CX Amsterdam The Netherlands Tel.: ++ 20 512 7986 Fax: ++ 20 669 1383 email: lpa...@xs4all.nl ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel