[BioC] Quick start to linking GO terms and microarray data

[michael watson (IAH-C)]

Hi

I want to investigate the GO terms associated with my microarray data
(normally, a list of genes from topTable() in limma)

I have read the vignettes for goTools and GOStats, and to be honest, I
am still a little unclear what the overall process is, particularly if I
am working with a custom array and not with affy or operon.

Lets say, for example, I have my array data in a data.frame containing
gene names.  In a separate data frame I have a link between my gene
names and LocusLink IDs.  How do I:

1) Find the GO terms associated with subsets of my genes? (I realise I
can use merge() to link my array data to the LocusLink ids, but what do
I do then?)

2) Fins out if a particular GO term is statistically over-represented in
a particular group

Finally, is the only way to link into GO through LocusLink identifiers?

Many thanks
Mick