[BioC] How are GO2PROBE built

[Marc Carlson]

Hi John,

The annotation system is not meant to be ad hoc although it has been
changing a lot recently as we have migrated to a much more powerful
database centric system.  Please have a look at the vignettes on this
page to see more current information:

http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html

Please let me know if you have any further questions.


  Marc



john seers (IFR) wrote:
>  
>
> Hi Sean
>
> Turning this into a more general question. Whenever I have to deal with
> a new type of Affymetrix array I seem to have to root around
> Bioconductor packages to find out how it is annotated etc. By the time I
> come around to do it again it has all changed and is done in a different
> way to how it was done before. My difficulty is it all feels a bit adhoc
> and comes at me in bits and pieces. Also I always feel there is probably
> a better way to do it that I am missing.
>
> Is there anywhere information that gives a better big picture that pulls
> it together a bit? What are the foundation designs/philosophy that all
> the packages are following? Is there a routemap type document that
> describes Bioconductor's approach to all this? 
>
> Any pointers to useful information gratefully received.
>
> Thanks.
>
>
> John Seers
>
>
>
>
>
>
>  
> ---
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Sean Davis
> Sent: 02 October 2008 11:55
> To: Oura Tomonori
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] How are GO2PROBE built
>
> 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
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>
>