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

[Saurin D. Jani]

Thanks for your reply and the lookUp function works and its good old cool function. But that function only gives GOIDs then for each GOID ..GO Term needs to be retrived and if some of the ProbeID does not have Terms ..I need to check for NA return value...which takes very long time for building  the Whole Chip's annotation matirx. and its same with PATH  as well. 

aaf.handler does the job fairly quickly..and do you know anything like that for illumina or for aglilant ? aaf.handler's output is also aaf.table class so, do you know how to convert aaf class table to data.frame or matrix?


Thank you,
Saurin




----- Original Message ----
From: Marc Carlson <mcarlson at fhcrc.org>
To: Saurin D. Jani <saurin_jani at yahoo.com>
Cc: Bioconductor mailing list <bioconductor at stat.math.ethz.ch>
Sent: Mon, December 21, 2009 8:05:01 PM
Subject: Re: [BioC] Probeid to GOTerms... from AnnotationDBI?

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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