
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
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