Hi Simon,

you can take a look at the topGO package. It analyzing the GO hierarchically
but in a bottom-up approach. Sections 2 and 3 from the vignette shows how
you can address question 1) and 2) using this package.

If you need some code-snippet for your problem, you can look at the
annFUN.hgu. But be careful that this function is providing only the most
specific annotations. For all genes/probes annotated to a GO term you need
to build a topGOdata object and use the function genesInTerm() to retrieve
the annotations.

Hope this helps,
Adrian



On 7/30/07, Simon Lin <simonlin@duke.edu> wrote:
>
> Hello,
>
> I am looking for some GO analysis code-snippet for the following task,
>
> 1) list all the GO terms under "molecular function"
> 2) For a given GO id, list the associated Entrez gene IDs (or Affymetrix
> probe IDs for U133A)
>
> A further question: is there a package analyzeing GO hierarchically? I
> mean,
> testing the parent nodes first; if it is not significant, then, testing
> the
> children? I think most of the packages just test all the GO terms
> simutanuously.
>
> Thanks!
>
> Simon
>
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