Dear List, I have been trying to use p.adjust() to do BH multiple test correction and have gotten some unexpected results. I thought that the equation for this was:
pBH = p*n/i where p is the original p value, n is the number of tests and i is the rank of the p value. However when I try and recreate the corrected p from my most significant value it does not match up to the one computed by the method p.adjust: > setwd("C:/work/Methylation/IMA/GM/siteLists") > > hypTable <- read.delim("hypernormal vs others.txt") > pList <- hypTable$p > names(pList) <- hypTable$site > > adjusted <- p.adjust(pList, method="BH") > adjusted[1] cg27433479 0.05030589 > > pList[1]*nrow(hypTable)/1 cg27433479 0.09269194 I tried to recreate this is a small example of a vector of 5 p values but everything worked as expected there. I was wondering if there is some subtle difference about how p.adjust operates? Is there something more complicated about how to calculate 'n' or 'i' - perhaps due to identical p values being assigned the same rank or something? Does anyone have an idea what might be going on here? Many thanks, Scott ______________________________________________ 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.