extracting probe sets corresponding to a given gene
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@christos-hatzis-1615
Last seen 10.2 years ago
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=""/>
Annotation probe Annotation probe • 887 views
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@james-w-macdonald-5106
Last seen 3 days ago
United States
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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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
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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
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@christos-hatzis-1615
Last seen 10.2 years ago
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
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