[BioC] GO annotations

[Marc Carlson]

Hi Maura,

I am sorry that your question is a little opaque to me so I will guess
from you code that you are trying to get GO annotations for probesets? 
In addition to biomaRt, you could use one of the affy chip annotation
packages that we have here (depending which platform you needed).

http://www.bioconductor.org/packages/devel/data/annotation/html/ag.db.html

http://www.bioconductor.org/packages/devel/data/annotation/html/ath1121501.db.html

If it was data about the internal structure of GO that you wanted, you
could use GO.db.

http://www.bioconductor.org/packages/devel/data/annotation/html/GO.db.html

Hope this answers your questions,


  Marc



mauede at alice.it wrote:
> I succeeded in retrieving data from dataset  athaliana_gene_ensembl (see the following example).
>
> But I do not know how to retrieve the GO annotations using function getBM.
>
> I mean, I do not know which attributes return the GO information for item in such a dataset.
>
> Any halp is more than welcome. 
>
> Thank you in advance,
>
> Maura
>
>   
>> gramene<-useMart('ENSEMBL_MART_ENSEMBL',dataset="athaliana_gene_ensembl")
>>     
> Checking attributes ... ok
> Checking filters ... ok
>
> # EXAMPLE
>   
>> go<-getBM(attributes="ensembl_gene_id",values="245042_at",filters="affy_ath1", mart=gramene)
>> go
>>     
>    ensembl_gene_id
> 1 AT2G26540-TAIR-G
>
>
>
>
> .html?pmk=footer> 
>
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>
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