[BioC] Probeid to GOTerms... from AnnotationDBI?

[Marc Carlson]

How about:

myGeneNames <- lookUp(Probeids, chiptype, 'GO')
myGeneNames <- lookUp(Probeids, chiptype, 'PATH')


For documentation see:

?chiptypePATH
and
?chiptypeGO

Where "chiptype" is the name of your annotation package.  "hgu95av2" for
example would be the "chiptype" for the hgu95av2.db package.


  Marc




Saurin D. Jani wrote:
> Hi BioC,
>
> is there anyway, I can query AnnotationDBI to pull out All KEGG Pathway names and All GO Terms associated with a ProbeID similarly what I am doing for GENENAME or SYM...!! ?
>
> I can pull all GeneNames from ProbeID:
>
> For Illumina Arrays:
>
> myGeneNames <- lookUp(nu_IDs, chiptype, 'SYMBOL');
> myGeneNames <- lookUp(nu_IDs, chiptype, 'GENENAME');
>
> For Affymetrix or Agilnat arrays:
>
> myGeneNames <- lookUp(Probeids, chiptype, 'SYMBOL');
> myGeneNames <- lookUp(Probeids, chiptype, 'GENENAME')
>
>
> Then I do Column Bind...for all my probeds to GeneNames....
>
> My_Annotation_Matrix <- cbind(Probeids,myGeneSymbos,myGeneNames);
>
> Now, I would like to put KEGG pathway names and GO Terms...!! 
>
> For Affymetrix arrays: aaf.handler does the JOB but..it outputs aaf table and ..how to convert them to Matrix..or data.frame....does any one know?
>
> Thank you so much in advance,
> Saurin
>
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