[BioC] Annotation

Seth Falcon sfalcon at fhcrc.org
Thu Jul 13 22:02:07 CEST 2006

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
>> annotation(exprSet.object)
> and it R will give you the annotation key for the corresponding LocusLink
> ID.  

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?

The probe ID ==> EntrezGene ID mapping is chip dependent.  For
many Affymetrix chips, there is a BioC annotationd data package
available.  That is not the case for two-color chips.

+ seth

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