Dear list, I have performed several tests for the hypergeometric distribution using phyper() for some gene annotation categories as follows
>phyper(26,830,31042,337, lower.tail=F) >phyper(16,387,31042,337, lower.tail=F) . . . I am only running some selected categories but I would like to correct this value for multiple testing since I have 3121 possible tests according to 3121 annotation categories. I think that for the case of Bonferroni corrections, I should correct this output by the total number of possible tests conducted (3121): >phyper(26,830,31042,337, lower.tail=F)*3121 >phyper(16,387,31042,337, lower.tail=F)*3121 But I would like to perform FDR, i.e. Benjamini correction. I know that multtest package has the function mt.rawp2adjp() but I would need to save all the p.values for the 3121 in a vector and use this as a parameter of the function. Is there another way of computing this adjusted p.value for only some of the categories? Thanks for your help, David (R version 2.6.0) (Windows OS) ______________________________________________ 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.
