[BioC] How are GO2PROBE built

[Sean Davis]

On Thu, Oct 2, 2008 at 3:11 AM, Oura Tomonori <tomonori.oura at gmail.com> wrote:
> Dear BioC,
>
> How are the mappings of Affymetrix probe ids to Gene Ontology terms in
> metadata package provided by Bioconductor build?
>
> I am trying to use some gene set analysis packages and find some
> pakage use the *GO2PROBE (ex. hgu133aGO2PROBE) information, but
> another package use the external gene set definition, such as MSigDB.
>
> So I want to know the criteria for select specific GO term among
> possible terms for each probe id in Bioconductor.
> I already read the documents about AnnBuilder package, however.

To make a long story short, the annotations available from affy are
mapped to Entrez Gene IDs.  Then, the information from Entrez Gene--in
this case, gene ontology--is mapped to affy id.  The dates associated
with the data, the source of the data, and how the data are mapped
will all affect the final mapping of affy ID to gene ontology.  The
nice thing about gene ontology analyses is that they are typically
based on "sets" of genes making it much less important to start with
EXACTLY the same gene ontology mappings.  In fact, in practice, it
will be pretty difficult to do so.

If you want to see the details of the current Bioconductor annotation
package build process, you want to read the AnnotationDbi SQLForge
vignette, as AnnBuilder is outdated.

Finally, if I have misunderstood your question, perhaps you could clarify.

Sean