[BioC] extracting probe sets corresponding to a given gene

[Christos Hatzis]

Excuse my misspelling below.  The gene symbol should be ESR1 (estrogen
receptor 1) instead of ERS1.  However the result is the same.

> get("ESR1",hgu133aSYMBOL)
Error in get(x, envir, mode, inherits) : variable "ESR1" was not found

-Christos

-----Original Message-----
From: Christos Hatzis [mailto:christos at silicoinsights.com] 
Sent: Monday, February 20, 2006 10:47 AM
To: 'James W. MacDonald'
Cc: 'bioconductor at stat.math.ethz.ch'
Subject: RE: [BioC] extracting probe sets corresponding to a given gene

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.

Thanks.
-Christos

-----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?

Yup,

get("ESR1", hgu133aSYMBOL)

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

HTH,

Jim


--
James W. MacDonald, M.S.
Biostatistician
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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