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

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

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

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 | +--------------------------------------------------------------------- ------+