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

[Wolfgang Huber]

Johannes Graumann wrote:
> 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

Dear Johannes,

not sure whether the existing software provides directly for your
question, or whether indeed I fully understand your question, but if I
do, one option would be simply to do a Binomial test against the Null
hypothesis

    a[i]  ~  Bin( a[i]+b[i], p=0.5)

where

 a[i] : frequency of GO Term i in Experiment A
 b[i] : frequency of GO Term i in Experiment B

This can be done just using the function "pbinom". Or to consider the
z-scores

  (a-b) / sqrt(a+b)


Best wishes
 Wolfgang

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Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber