[BioC] Annotation

Sean Davis sdavis2 at mail.nih.gov
Thu Jul 13 22:22:58 CEST 2006

Seth Falcon wrote:
> Hi Justin,
> jmungal at berkeley.edu writes:
>>Hello, I am an undergraduate doing summer research at Stanford University.
>> I've downloaded a few GSP files from GEO and converted them to the class
>>exprSet.  Typically with an object of class exprSet you can simply type
>>and it R will give you the annotation key for the corresponding LocusLink
> I'm not so sure about that.  The annotation() method for the exprSet
> class is AFAIK a simple accessor for the annotation slot of said
> class.  This slot is intended to hold a string naming the annotation
> package appropriate for the data contained in the exprSet.
>>However, with the data sets I have, there is no annotation.  Does
>>anyone know an easy way of finding the LocusLink ID's for such a
>>data set?


I don't think there is such a thing as a GSP from GEO.  If you clarify 
what you mean by GSP, I might be able to help you get the associated 
platform (GPL) information from GEO using GEOquery.  You can then use 
that information for your annotation (which may or may not satisfy your 
needs, depending on what is available in the GPL).


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