[BioC] NEwbie: How to determine significant enrichment differences of GO term vectors?

[Johannes Graumann]

Hello,

Please excuse this naive question, but I would appreciate if someone could
point me at the right function(s) to use:
I have two vectors containing all GO terms associated with proteins
retrieved in two proteomic experiments and would like to figure out for
which categories they differ significantly from each other. I am obviously
somewhat limited by the fact of not being able to use the 'standard'
annotation packages, but I have build my own protein -> GenBank -> GO
package using AnnBuilder.

Please let me know how you would tackle this.

Thanks for your patience,

Joh