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
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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
> _________________________________________________________________
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> Indiana Jones prizes with Live Search
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> [[alternative HTML version deleted]]
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PO Box 19024 Seattle, WA 98109
Location: Arnold Building M2 B169
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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
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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
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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
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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