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?
Thank you.
Christos Hatzis, Ph.D.
Vice President, Technology
Nuvera Biosciences, Inc.
400 West Cummings Park
Suite 5350
Woburn, MA 01801
Tel: 781-938-3830
www.nuverabio.com <http: www.nuverabio.com=""/>
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
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@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
Christos Hatzis wrote:
> 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.
Hmmm. Maybe I need to take up drinking coffee ;-D
Anyway, what you want to do is really the reverse of what the
environment is set up to do, so I think your solution is about as
elegant as it gets.
Best,
Jim
>
> Thanks.
> -Christos
>
--
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
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@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@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
