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Ruppert Valentino | 15 May 15:38

Re: converting gene name to affy probe


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@...> To:
ruppert7@...> 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@...> >
https://stat.ethz.ch/mailman/listinfo/bioconductor> > Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor> >> >!
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James W. MacDonald | 15 May 16:06

Re: 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 <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,
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Ruppert Valentino | 16 May 00:27

Re: converting gene name to affy probe


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@...> To:
ruppert7@...> CC:
bioconductor@...> 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 <at> ifnotfound) :> value for
"DKFZp779B086" not found> > You can try the ALIAS2
 PROBE 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@...> To:
ruppert7@...> Subject: Re: [BioC] converting gene name to
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