[R] BH correction with p.adjust

[Scott Robinson]

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