[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.
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
734-647-5623
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