missing GO identifier in hgu133a GO
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Ken Stickler ▴ 20
@ken-stickler-101
Last seen 9.6 years ago
Hi, there is a missing GO id in hgu133a GO.xml <annbuilder:entry id="" describ="Gene Ontology identifier"> <annbuilder:item name="GO2AFFY" value="203787_at"/> <annbuilder:item name="GO2AFFY" value="210829_s_at"/> <annbuilder:item name="GO2AFFY" value="206134_at"/> <annbuilder:item name="GO2AFFY" value="208828_at"/> <annbuilder:item name="GO2AFFY" value="218527_at"/> <annbuilder:item name="GO2ALLAFFY" value="203787_at"/> <annbuilder:item name="GO2ALLAFFY" value="210829_s_at"/> <annbuilder:item name="GO2ALLAFFY" value="206134_at"/> <annbuilder:item name="GO2ALLAFFY" value="208828_at"/> <annbuilder:item name="GO2ALLAFFY" value="218527_at"/> <annbuilder:item name="AFFYCOUNTS" value="5"/> </annbuilder:entry> Also, is the GO file available for the hgu133b chip? Thanks, ken
GO hgu133a hgu133b GO hgu133a hgu133b • 1.1k views
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John Zhang ★ 2.9k
@john-zhang-6
Last seen 9.6 years ago
Thank you for reporting the error! I will have a look to find out what might have been wrong. We do not have the annotation for hgu133b chip yet but will try to includ it in the future. >From: Ken Stickler <kestickler@attbi.com> >To: bioconductor@stat.math.ethz.ch >X-Priority: 3 (Normal) >MIME-Version: 1.0 >Subject: [BioC] missing GO identifier in hgu133a GO >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.0.13 >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Subscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> >List-Archive: <http: www.stat.math.ethz.ch="" pipermail="" bioconductor=""/> >Date: Fri, 25 Oct 2002 12:27:53 -0400 > >Hi, > >there is a missing GO id in hgu133a GO.xml > ><annbuilder:entry id="" describ="Gene Ontology identifier"> > <annbuilder:item name="GO2AFFY" value="203787_at"/> > <annbuilder:item name="GO2AFFY" value="210829_s_at"/> > <annbuilder:item name="GO2AFFY" value="206134_at"/> > <annbuilder:item name="GO2AFFY" value="208828_at"/> > <annbuilder:item name="GO2AFFY" value="218527_at"/> > <annbuilder:item name="GO2ALLAFFY" value="203787_at"/> > <annbuilder:item name="GO2ALLAFFY" value="210829_s_at"/> > <annbuilder:item name="GO2ALLAFFY" value="206134_at"/> > <annbuilder:item name="GO2ALLAFFY" value="208828_at"/> > <annbuilder:item name="GO2ALLAFFY" value="218527_at"/> > <annbuilder:item name="AFFYCOUNTS" value="5"/> ></annbuilder:entry> > > >Also, is the GO file available for the hgu133b chip? > >Thanks, > >ken > > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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Ken Stickler ▴ 20
@ken-stickler-101
Last seen 9.6 years ago
Hi John, are there notes somewhere on how the annotations were built? Maybe i could try repeating it for hgu133b. Also interested in the mouse chips. Thanks. John Zhang wrote: > > Thank you for reporting the error! I will have a look to find out what might > have been wrong. We do not have the annotation for hgu133b chip yet but will try > to includ it in the future. > > >From: Ken Stickler <kestickler@attbi.com> > >To: bioconductor@stat.math.ethz.ch > >X-Priority: 3 (Normal) > >MIME-Version: 1.0 > >Subject: [BioC] missing GO identifier in hgu133a GO > >X-BeenThere: bioconductor@stat.math.ethz.ch > >X-Mailman-Version: 2.0.13 > >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> > >List-Post: <mailto:bioconductor@stat.math.ethz.ch> > >List-Subscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, > <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> > >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> > >List-Unsubscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, > <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> > >List-Archive: <http: www.stat.math.ethz.ch="" pipermail="" bioconductor=""/> > >Date: Fri, 25 Oct 2002 12:27:53 -0400 > > > >Hi, > > > >there is a missing GO id in hgu133a GO.xml > > > ><annbuilder:entry id="" describ="Gene Ontology identifier"> > > <annbuilder:item name="GO2AFFY" value="203787_at"/> > > <annbuilder:item name="GO2AFFY" value="210829_s_at"/> > > <annbuilder:item name="GO2AFFY" value="206134_at"/> > > <annbuilder:item name="GO2AFFY" value="208828_at"/> > > <annbuilder:item name="GO2AFFY" value="218527_at"/> > > <annbuilder:item name="GO2ALLAFFY" value="203787_at"/> > > <annbuilder:item name="GO2ALLAFFY" value="210829_s_at"/> > > <annbuilder:item name="GO2ALLAFFY" value="206134_at"/> > > <annbuilder:item name="GO2ALLAFFY" value="208828_at"/> > > <annbuilder:item name="GO2ALLAFFY" value="218527_at"/> > > <annbuilder:item name="AFFYCOUNTS" value="5"/> > ></annbuilder:entry> > > > > > >Also, is the GO file available for the hgu133b chip? > > > >Thanks, > > > >ken > > > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor@stat.math.ethz.ch > >http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
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rgentleman ★ 5.5k
@rgentleman-7725
Last seen 8.9 years ago
United States
Hi Ken, All the data packages are built with AnnBuilder (available with documentation from Bioconductor). Robert On Mon, Oct 28, 2002 at 04:05:38PM -0500, Ken Stickler wrote: > Hi John, > > are there notes somewhere on how the annotations were built? Maybe i could try repeating it for hgu133b. Also interested in the mouse chips. > Thanks. > > John Zhang wrote: > > > > Thank you for reporting the error! I will have a look to find out what might > > have been wrong. We do not have the annotation for hgu133b chip yet but will try > > to includ it in the future. > > > > >From: Ken Stickler <kestickler@attbi.com> > > >To: bioconductor@stat.math.ethz.ch > > >X-Priority: 3 (Normal) > > >MIME-Version: 1.0 > > >Subject: [BioC] missing GO identifier in hgu133a GO > > >X-BeenThere: bioconductor@stat.math.ethz.ch > > >X-Mailman-Version: 2.0.13 > > >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> > > >List-Post: <mailto:bioconductor@stat.math.ethz.ch> > > >List-Subscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, > > <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> > > >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> > > >List-Unsubscribe: <http: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, > > <mailto:bioconductor- request@stat.math.ethz.ch?subject="unsubscribe"> > > >List-Archive: <http: www.stat.math.ethz.ch="" pipermail="" bioconductor=""/> > > >Date: Fri, 25 Oct 2002 12:27:53 -0400 > > > > > >Hi, > > > > > >there is a missing GO id in hgu133a GO.xml > > > > > ><annbuilder:entry id="" describ="Gene Ontology identifier"> > > > <annbuilder:item name="GO2AFFY" value="203787_at"/> > > > <annbuilder:item name="GO2AFFY" value="210829_s_at"/> > > > <annbuilder:item name="GO2AFFY" value="206134_at"/> > > > <annbuilder:item name="GO2AFFY" value="208828_at"/> > > > <annbuilder:item name="GO2AFFY" value="218527_at"/> > > > <annbuilder:item name="GO2ALLAFFY" value="203787_at"/> > > > <annbuilder:item name="GO2ALLAFFY" value="210829_s_at"/> > > > <annbuilder:item name="GO2ALLAFFY" value="206134_at"/> > > > <annbuilder:item name="GO2ALLAFFY" value="208828_at"/> > > > <annbuilder:item name="GO2ALLAFFY" value="218527_at"/> > > > <annbuilder:item name="AFFYCOUNTS" value="5"/> > > ></annbuilder:entry> > > > > > > > > >Also, is the GO file available for the hgu133b chip? > > > > > >Thanks, > > > > > >ken > > > > > > > > >_______________________________________________ > > >Bioconductor mailing list > > >Bioconductor@stat.math.ethz.ch > > >http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+
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