[BioC] extracting probe sets corresponding to a given gene

Christos Hatzis christos at silicoinsights.com
Mon Feb 20 16:47:11 CET 2006

Hi Jim,

This is what I tried first, but I get an error:

> get("ERS1",hgu133aSYMBOL)
Error in get(x, envir, mode, inherits) : variable "ERS1" was not found

I think "get" works in the reverse direction, i.e. to find a gene symbol
that corresponds to a given probe set.  I actually needed the opposite, i.e.
given a gene, find all the probe sets from that gene on the chip.


-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
Sent: Monday, February 20, 2006 8:42 AM
To: christos at silicoinsights.com
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] extracting probe sets corresponding to a given gene

Hi Christos,

Christos Hatzis wrote:
> Hello,
> I am working through the annotation packages and trying to find a way 
> to extract the probe sets that correspond to a given gene.  I have 
> come up with the following, which does not look very direct:
> as.list(hgu133aSYMBOL)[ as.list(hgu133aSYMBOL) == "ESR1" ]
> Is there a more efficient way to do this?


get("ESR1", hgu133aSYMBOL)

You can use mget() to get() multiple values as well.



James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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