Question: GOstats and GenePix arrays

0

Jacob Michaelson •

**320**wrote:Hi all,
I'm trying to use the "guts" of the GOHyperG function in GOstats as a
basis for a similar function for GenePix data. I've found a basic
description of the phyper function in the context of GO:
# How to implement phyper function for GO analysis
# phyper(x-1, m, n-m , k, lower.tail = FALSE)
# x: number of sample genes at GO node (can be vector with many
entries)
# m: number of genes at GO node (works with vector of same
length
as x)
# n: number of unique genes at all GO nodes
# k: number of unique genes in test sample that have GO mappings
Values for x and k seem straightforward, but I'm wondering about m and
n. The arrays we're working with seem to have fewer genes on them
than
the total number cataloged in the organism's online databases. So
should m and n be based on the absolute total number of genes
annotated,
or the number of genes annotated *on the chip*?
Thanks in advance,
Jake