converting gene name to affy probe
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@ruppert-valentino-1376
Last seen 9.6 years ago
Hello, I am trying to convert a file of gene names to corresponding affy probe names. I managed to write a script that puts the genes in an array then I use the feat = getFeature(symbol = gensym, type = "affy_hg_u133a", mart = mart) in biomaRt however I seem to hit a snag when there is more than probe for a gene name. Does anyone know of an existing script that can do this? thanks Ruppert _________________________________________________________________ Win Indiana Jones prizes with Live Search [[alternative HTML version deleted]]
probe convert biomaRt probe convert biomaRt • 1.9k views
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@martin-morgan-1513
Last seen 6 weeks ago
United States
Hi Ruppert -- The annotation package hgu133a.db contains a 'map' from probe id to symbol (I guess this is what you mean by 'gene name') > library(hgu133a.db) > ls(2) [1] "hgu133a" "hgu133aACCNUM" "hgu133aALIAS2PROBE" [4] "hgu133aCHR" "hgu133aCHRLENGTHS" "hgu133aCHRLOC" [7] "hgu133a_dbconn" "hgu133a_dbfile" "hgu133a_dbInfo" [10] "hgu133a_dbschema" "hgu133aENSEMBL" "hgu133aENSEMBL2PROBE" [13] "hgu133aENTREZID" "hgu133aENZYME" "hgu133aENZYME2PROBE" [16] "hgu133aGENENAME" "hgu133aGO" "hgu133aGO2ALLPROBES" [19] "hgu133aGO2PROBE" "hgu133aMAP" "hgu133aMAPCOUNTS" [22] "hgu133aOMIM" "hgu133aORGANISM" "hgu133aPATH" [25] "hgu133aPATH2PROBE" "hgu133aPFAM" "hgu133aPMID" [28] "hgu133aPMID2PROBE" "hgu133aPROSITE" "hgu133aREFSEQ" [31] "hgu133aSYMBOL" "hgu133aUNIGENE" You'd like to reverse the map so it goes from SYMBOL to probe id > rmap = revmap(hgu133aSYMBOL) and then look up all your symbols > syms = c("NAT1", "TCF3") > mget(syms, rmap) $NAT1 [1] "214440_at" $TCF3 [1] "209151_x_at" "209152_s_at" "209153_s_at" "210776_x_at" "213730_x_at" [6] "213731_s_at" "213732_at" "213809_x_at" "213811_x_at" "215260_s_at" [11] "216645_at" "216647_at" Not sure where you want to go from here, though? Martin Ruppert Valentino <ruppert7 at="" hotmail.com=""> writes: > Hello, I am trying to convert a file of gene names to corresponding > affy probe names. I managed to write a script that puts the genes in > an array then I use the feat = getFeature(symbol = gensym, type = > "affy_hg_u133a", mart = mart) in biomaRt however I seem to hit a snag > when there is more than probe for a gene name. Does anyone know of an > existing script that can do this? thanks Ruppert > _________________________________________________________________ Win > Indiana Jones prizes with Live Search > > [[alternative HTML version deleted]] > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793
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@ruppert-valentino-1376
Last seen 9.6 years ago
Hello, I am trying to convert a file of gene names to corresponding affy probe names. I managed to write a script that puts the genes in an array then I use the feat = getFeature(symbol = gensym, type = "affy_hg_u133a", mart = mart) in biomaRt however I seem to hit a snag when there is more than probe for a gene name. Does anyone know of an existing script that can do this? thanks Ruppert _________________________________________________________________ Great deals on almost anything at eBay.co.uk. Search, bid, find and win on [[alternative HTML version deleted]]
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@ruppert-valentino-1376
Last seen 9.6 years ago
Hi Sebastien, Thanks for the tip : ls(hgu133aSYMBOL)[mget(ls(hgu133aSYMBOL), hgu133aSYMBOL) %in% gensym] works fine I would be grateful if you can tell me how to convert Affy probe to gene name? i.e. the opposite way I tried using hgu133aGENENAME but that didn't work as its using the description. How do I use hgu133aSYMBOL to get gene name from affy probe. Many thanks Ruppert > Date: Tue, 6 May 2008 13:07:22 +1000> From: seb@gerega.net> To: ruppert7@hotmail.com> Subject: Re: [BioC] converting gene name to affy probe> > Ruppert Valentino wrote:> > Hello, I am trying to convert a file of gene names to corresponding affy probe names. I managed to write a script that puts the genes in an array then I use the feat = getFeature(symbol = gensym, type = "affy_hg_u133a", mart = mart) in biomaRt however I seem to hit a snag when there is more than probe for a gene name. Does anyone know of an existing script that can do this? thanks Ruppert> > _________________________________________________________________> > Win Indiana Jones prizes with Live Search> >> > [[alternative HTML version deleted]]> >> > _______________________________________________> > Bioconductor mailing list> > Bioconductor@stat.math.ethz.ch> > https://stat.ethz.ch/mailman/listinfo/bioconductor> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor> >> > > > I think this should do what you want:> library(hgu133a.db)> ls(hgu133aSYMBOL)[mget(ls(hgu133aSYMBOL), hgu133aSYMBOL) %in% gensym]> > hope that helps,> Sebastien _________________________________________________________________ Be a Hero and Win with Iron Man [[alternative HTML version deleted]]
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Actually, that isn't what you want. That's like driving a nail with the butt-end of a screwdriver. It will eventually do what you want, but that hammer sitting there is much more efficient. ;-D > get("VEGFA", revmap(hgu133aSYMBOL)) [1] "210512_s_at" "210513_s_at" "211527_x_at" "212171_x_at" And to get the symbol, given the probe ID > get("210512_s_at", hgu133aSYMBOL) [1] "VEGFA" or if the symbol you have is not found: > get("DKFZp779B086", revmap(hgu133aSYMBOL)) Error in .checkKeys(value, Rkeys(x), x at ifnotfound) : value for "DKFZp779B086" not found You can try the ALIAS2PROBE mapping: > get("DKFZp779B086", hgu133aALIAS2PROBE) [1] "217757_at" Or you could just start with the ALIAS2PROBE, since it contains all the available symbols. > get("VEGFA", hgu133aALIAS2PROBE) [1] "210512_s_at" "210513_s_at" "211527_x_at" "212171_x_at" Best, Jim Ruppert Valentino wrote: > Hi Sebastien, > > Thanks for the tip : > > ls(hgu133aSYMBOL)[mget(ls(hgu133aSYMBOL), hgu133aSYMBOL) %in% gensym] > works fine > > I would be grateful if you can tell me how to convert Affy probe to gene name? i.e. the opposite way > > I tried using hgu133aGENENAME but that didn't work as its using the description. > > How do I use hgu133aSYMBOL to get gene name from affy probe. > > Many thanks > > Ruppert > >> Date: Tue, 6 May 2008 13:07:22 +1000> From: seb at gerega.net> To: ruppert7 at hotmail.com> Subject: Re: [BioC] converting gene name to affy probe> > Ruppert Valentino wrote:> > Hello, I am trying to convert a file of gene names to corresponding affy probe names. I managed to write a script that puts the genes in an array then I use the feat = getFeature(symbol = gensym, type = "affy_hg_u133a", mart = mart) in biomaRt however I seem to hit a snag when there is more than probe for a gene name. Does anyone know of an existing script that can do this? thanks Ruppert> > _________________________________________________________________> > Win Indiana Jones prizes with Live Search> >> > [[alternative HTML version deleted]]> >> > _______________________________________________> > Bioconductor mailing list> > Bioconductor at stat.math.ethz.ch> > https://stat.ethz.ch/mailman/listinfo/bioconductor> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor> >> >! > > > I think this should do what you want:> library(hgu133a.db)> ls(hgu133aSYMBOL)[mget(ls(hgu133aSYMBOL), hgu133aSYMBOL) %in% gensym]> > hope that helps,> Sebastien > _________________________________________________________________ > Be a Hero and Win with Iron Man > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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, thanks for the advise the problem here is I have a list of genes and if I use mget instead of get then it give me a list so what i like to do is to convert list of genes to their probes but based on what you mentioned its not hard to get it to work. thanks Ruppert> Date: Thu, 15 May 2008 10:06:03 -0400> From: jmacdon@med.umich.edu> To: ruppert7@hotmail.com> CC: bioconductor@stat.math.ethz.ch> Subject: Re: [BioC] converting gene name to affy probe> > Actually, that isn't what you want. That's like driving a nail with the > butt-end of a screwdriver. It will eventually do what you want, but that > hammer sitting there is much more efficient. ;-D> > > get("VEGFA", revmap(hgu133aSYMBOL))> [1] "210512_s_at" "210513_s_at" "211527_x_at" "212171_x_at"> > And to get the symbol, given the probe ID> > > get("210512_s_at", hgu133aSYMBOL)> [1] "VEGFA"> > or if the symbol you have is not found:> > > get("DKFZp779B086", revmap(hgu133aSYMBOL))> Error in .checkKeys(value, Rkeys(x), x@ifnotfound) :> value for "DKFZp779B086" not found> > You can try the ALIAS2PROBE mapping:> > > get("DKFZp779B086", hgu133aALIAS2PROBE)> [1] "217757_at"> > Or you could just start with the ALIAS2PROBE, since it contains all the > available symbols.> > > get("VEGFA", hgu133aALIAS2PROBE)> [1] "210512_s_at" "210513_s_at" "211527_x_at" "212171_x_at"> > Best,> > Jim> > > Ruppert Valentino wrote:> > Hi Sebastien,> > > > Thanks for the tip :> > > > ls(hgu133aSYMBOL)[mget(ls(hgu133aSYMBOL), hgu133aSYMBOL) %in% gensym]> > works fine> > > > I would be grateful if you can tell me how to convert Affy probe to gene name? i.e. the opposite way> > > > I tried using hgu133aGENENAME but that didn't work as its using the description. > > > > How do I use hgu133aSYMBOL to get gene name from affy probe.> > > > Many thanks> > > > Ruppert> > > >> Date: Tue, 6 May 2008 13:07:22 +1000> From: seb@gerega.net> To: ruppert7@hotmail.com> Subject: Re: [BioC] converting gene name to affy probe> > Ruppert Valentino wrote:> > Hello, I am trying to convert a file of gene names to corresponding affy probe names. I managed to write a script that puts the genes in an array then I use the feat = getFeature(symbol = gensym, type = "affy_hg_u133a", mart = mart) in biomaRt however I seem to hit a snag when there is more than probe for a gene name. Does anyone know of an existing script that can do this? thanks Ruppert> > _________________________________________________________________> > Win Indiana Jones prizes with Live Search> >> > [[alternative HTML version deleted]]> >> > _______________________________________________> > Bioconductor mailing list> > Bioconductor@stat.math.ethz.ch> > https://stat.ethz.ch/mailman/listinfo/bioconductor> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor> >> > >!> > > > I think this should do what you want:> library(hgu133a.db)> ls(hgu133aSYMBOL)[mget(ls(hgu133aSYMBOL), hgu133aSYMBOL) %in% gensym]> > hope that helps,> Sebastien> > _________________________________________________________________> > Be a Hero and Win with Iron Man> > > > [[alternative HTML version deleted]]> > > > _______________________________________________> > Bioconductor mailing list> > Bioconductor@stat.math.ethz.ch> > https://stat.ethz.ch/mailman/listinfo/bioconductor> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor> > -- > 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 _________________________________________________________________ Win Indiana Jones prizes with Live Search [[alternative HTML version deleted]]
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