[BioC] converting gene name to affy probe

[James W. MacDonald]

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
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-- 
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