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)
