[BioC] GOstats and GenePix arrays

[Jake]

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