Hi all, I am trying to analyze data from the affy-chips rae230a and rae230b. Analysis seems to be ok but the annotation using annaffy and rae230a/b data packages 1.3.0 looks wrong. E.g. the rae230aSYMBOL environment holds the symbol A1BG for most of the affy ids. Does anybody have an idea what is going wrong? Claudio

Hi Claudio, I found the same problems with rae230a. Reinhold On Sun, 2003-08-24 at 18:46, Claudio Lottaz wrote: > Hi all, > I am trying to analyze data from the affy-chips rae230a and rae230b. > Analysis seems to be ok but the annotation using annaffy and rae230a/b > data packages 1.3.0 looks wrong. E.g. the rae230aSYMBOL environment > holds the symbol A1BG for most of the affy ids. Does anybody have an > idea what is going wrong? > Claudio -- Reinhold Koch <reinhold.koch@unibas.ch>

I will have a look at the data package and find/fix the bugs. Thank you for reporting. >Date: Sun, 24 Aug 2003 18:46:37 +0200 >From: Claudio Lottaz <claudio.lottaz@molgen.mpg.de> >X-Accept-Language: en >MIME-Version: 1.0 >To: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch> >Content-Transfer-Encoding: 7bit >X-AntiAbuse: This header was added to track abuse, please include it with any abuse report >X-AntiAbuse: Primary Hostname - server7.hostpoint.ch >X-AntiAbuse: Original Domain - stat.math.ethz.ch >X-AntiAbuse: Originator/Caller UID/GID - [47 12] / [47 12] >X-AntiAbuse: Sender Address Domain - molgen.mpg.de >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Spam-Status: No, hits=1.3 required=5.0 tests=BAYES_30, RCVD_IN_NJABL, RCVD_IN_OSIRUSOFT_COM, TO_ADDRESS_EQ_REAL, USER_AGENT_MOZILLA_XM, X_ACCEPT_LANG version=2.54 >X-Spam-Level: * >X-Spam-Checker-Version: SpamAssassin 2.54 (1.174.2.17-2003-05-11-exp) >Subject: [BioC] rae230a/b data packages buggy? >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.1.2 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Subscribe: <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >List-Archive: <https: www.stat.math.ethz.ch="" pipermail="" bioconductor=""> >List-Unsubscribe: <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> > >Hi all, >I am trying to analyze data from the affy-chips rae230a and rae230b. >Analysis seems to be ok but the annotation using annaffy and rae230a/b >data packages 1.3.0 looks wrong. E.g. the rae230aSYMBOL environment >holds the symbol A1BG for most of the affy ids. Does anybody have an >idea what is going wrong? >Claudio > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

I have found the bug. We are using an unified approach to get mappings between probe ids and LocusLink ids. Some of the probe ids that do not get mapped to a LocusLink id by any of the sources used were somehow mapped to LocusLink id "1". Thus, mappings for probes that are mapped to LocusLink id "1" are incorrect. Other mappings seem to be correct base on my limited checking results. I will fix the bug and have the correct data packages built as soon as I can. Sorry for the error. >Subject: Re: [BioC] rae230a/b data packages buggy? >From: Reinhold Koch <reinhold.koch@unibas.ch> >To: Claudio Lottaz <claudio.lottaz@molgen.mpg.de> >Mime-Version: 1.0 >Date: 25 Aug 2003 09:27:53 +0200 >Content-Transfer-Encoding: 7bit >X-Virus-Scan: vilter >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >X-Spam-Status: No, hits=-9.4 required=5.0 tests=BAYES_01, EMAIL_ATTRIBUTION, IN_REP_TO, QUOTED_EMAIL_TEXT, REFERENCES, REPLY_WITH_QUOTES, USER_AGENT_XIMIAN autolearn=ham version=2.54 >X-Spam-Level: >X-Spam-Checker-Version: SpamAssassin 2.54 (1.174.2.17-2003-05-11-exp) >Cc: bioconductor <bioconductor@stat.math.ethz.ch> >X-BeenThere: bioconductor@stat.math.ethz.ch >X-Mailman-Version: 2.1.2 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >List-Post: <mailto:bioconductor@stat.math.ethz.ch> >List-Subscribe: <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >List-Archive: <https: www.stat.math.ethz.ch="" pipermail="" bioconductor=""> >List-Unsubscribe: <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> > >Hi Claudio, > >I found the same problems with rae230a. > >Reinhold >On Sun, 2003-08-24 at 18:46, Claudio Lottaz wrote: >> Hi all, >> I am trying to analyze data from the affy-chips rae230a and rae230b. >> Analysis seems to be ok but the annotation using annaffy and rae230a/b >> data packages 1.3.0 looks wrong. E.g. the rae230aSYMBOL environment >> holds the symbol A1BG for most of the affy ids. Does anybody have an >> idea what is going wrong? >> Claudio > >-- >Reinhold Koch <reinhold.koch@unibas.ch> > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

I will. >Date: Mon, 25 Aug 2003 18:57:46 +0200 >From: Claudio Lottaz <claudio.lottaz@molgen.mpg.de> >User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.3) Gecko/20030312 >X-Accept-Language: en-us, en >MIME-Version: 1.0 >To: John Zhang <jzhang@jimmy.harvard.edu> >Subject: Re: [BioC] rae230a/b data packages buggy? >X-Enigmail-Version: 0.74.3.0 >X-Enigmail-Supports: pgp-inline, pgp-mime >Content-Transfer-Encoding: 7bit > >That's great news, thanks for the effort. >It would be great if you could tell me or the >list when the corrected data package >becomes available. >Claudio > >John Zhang wrote: > >>I have found the bug. We are using an unified approach to get mappings between >>probe ids and LocusLink ids. Some of the probe ids that do not get mapped to a >>LocusLink id by any of the sources used were somehow mapped to LocusLink id "1". >>Thus, mappings for probes that are mapped to LocusLink id "1" are incorrect. >>Other mappings seem to be correct base on my limited checking results. >> >>I will fix the bug and have the correct data packages built as soon as I can. >>Sorry for the error. >> >> >> >> >>>Subject: Re: [BioC] rae230a/b data packages buggy? >>>From: Reinhold Koch <reinhold.koch@unibas.ch> >>>To: Claudio Lottaz <claudio.lottaz@molgen.mpg.de> >>>Mime-Version: 1.0 >>>Date: 25 Aug 2003 09:27:53 +0200 >>>Content-Transfer-Encoding: 7bit >>>X-Virus-Scan: vilter >>>X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >>>X-Virus-Scanned: by amavisd-milter (http://amavis.org/) >>>X-Spam-Status: No, hits=-9.4 required=5.0 tests=BAYES_01, EMAIL_ATTRIBUTION, >>> >>> >>IN_REP_TO, QUOTED_EMAIL_TEXT, REFERENCES, REPLY_WITH_QUOTES, USER_AGENT_XIMIAN >>autolearn=ham version=2.54 >> >> >>>X-Spam-Level: >>>X-Spam-Checker-Version: SpamAssassin 2.54 (1.174.2.17-2003-05-11-exp) >>>Cc: bioconductor <bioconductor@stat.math.ethz.ch> >>>X-BeenThere: bioconductor@stat.math.ethz.ch >>>X-Mailman-Version: 2.1.2 >>>List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >>>List-Help: <mailto:bioconductor- request@stat.math.ethz.ch?subject="help"> >>>List-Post: <mailto:bioconductor@stat.math.ethz.ch> >>>List-Subscribe: <https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, >>> >>> >><mailto:bioconductor-request@stat.math.ethz.ch?subject=subscribe> >> >> >>>List-Archive: <https: www.stat.math.ethz.ch="" pipermail="" bioconductor=""> >>>List-Unsubscribe: >>> >>> >><https: www.stat.math.ethz.ch="" mailman="" listinfo="" bioconductor="">, >><mailto:bioconductor-request@stat.math.ethz.ch?subject=unsubscribe> >> >> >>>Hi Claudio, >>> >>>I found the same problems with rae230a. >>> >>>Reinhold >>>On Sun, 2003-08-24 at 18:46, Claudio Lottaz wrote: >>> >>> >>>>Hi all, >>>>I am trying to analyze data from the affy-chips rae230a and rae230b. >>>>Analysis seems to be ok but the annotation using annaffy and rae230a/b >>>>data packages 1.3.0 looks wrong. E.g. the rae230aSYMBOL environment >>>>holds the symbol A1BG for most of the affy ids. Does anybody have an >>>>idea what is going wrong? >>>>Claudio >>>> >>>> >>>-- >>>Reinhold Koch <reinhold.koch@unibas.ch> >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor@stat.math.ethz.ch >>>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >>> >>> >> >>Jianhua Zhang >>Department of Biostatistics >>Dana-Farber Cancer Institute >>44 Binney Street >>Boston, MA 02115-6084 >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor@stat.math.ethz.ch >>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >> >> >> > > >-- >--------------------------------------------------------------------- - >Claudio Lottaz >Max Planck Institute for Molecular Genetics >Computational Molecular Biology Department >Ihnestrasse 73, D-14195 Berlin (Germany) > >phone: +49 (0)30 8413 1177 > fax: +49 (0)30 8413 1176 > www: http://www.molgen.mpg.de/~lottaz > > Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084