[BioC] HyperGTest and genelists

[James W. MacDonald]

Hi David,

Does probeSetSummary() do what you want?

Best,

Jim



davidl at unr.nevada.edu wrote:
> Hello everyone,
> 
>       I like that the new HyperGTest function lets you specify the gene
> universe, get only the more specific GO terms in your results, and easily
> output a report with the expected counts, actual counts, and p values.  With
> the old GOHyperG results, I had written a function that retrieved the list of
> significant GOterms, found the gene names associated with those GO terms, and
> found the intersection of those gene names and my genes of interest.
> So my question is this:
> 
>     Is there a way to get the gene names of the genes of interest which were
> associated with the over or under represented GO terms found with HyperGTest? 
> I noticed there is a function for the GOHyperGResult object (geneIdUniverse)
> which retrieves the entrez gene identifiers from your gene universe for all the
> tested GO terms.  Is there a way to get only the entrez gene identifiers from
> your genes-of-interest group?  Could you then filter out the GO terms which did
> not meet the p-value cutoff?  Is there a function which could be applied to
> this list to change those entrez identifiers into gene names?  Or is there an
> easier way to get the names of the genes from your genes of interest which
> contributed to the "Count" column of the html report?  For example, if there
> was a method for retrieving the GO terms which met the p-value cutoff from the
> GOHyperGResult object, I could just use the function I've already written. 
> Thank you very much in advance for whatever help you can provide.  I really
> like the new hypergeometric function, and I hope this can be figured out.
> 
> Thank you,
> Dave
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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