[BioC] Retrieve GO terms for unanontaded organism and do enrichment by myself

[Ricardo Silva]

Hi,

I'm working with a fungus that don't have its genome sequenced. I have
a list of accession numbers from a proteomics experiment, and each
number come from a different organism.

For what I read until now, I found how to recover GO terms for
organism specific databases as in:

org.Mm.egGO[mappedLkeys(egids)]

is there a way to do this for a diverse group of accession numbers
from different organisms?

Assuming that I have my list of annotated GO terms the most simple way
to calculate the probability of "enrichment" of, lets say GOterm1
would be by:

phyper(9-1, 26, 825-26, 18, lower.tail=F)

where, 9 is number of times I saw the term on my sample,
26 is the total number of genes inside this classe (associated to GOterm1)??,
825 is the total number of genes inside all GO categories found?,
and 18 is my number of samples.

If any one knows a reference explaining each step I would appreciate
the reference, so that I could understand in details before using a
package.

thanks in advance for your help

Ricardo