Hi all, we found that there are about 8-9% of all probesets in the hgu133a package for which no information on chromosomal location (i.e. base pairs from the telomere) is available. However, other public databases like Golden Path offer start and end positions for each probeset on the array. What is the reason for this discrepancy ? What are the paths AnnBuilder uses in order to map probeset-IDs to chromosomal locations ? Would it be safe to use chromosomal locations obtained from other sources directly instead of relying on the hgu133a package ? Regards, Hilmar

AnnBuilder does use Golden Path for chromosomal locations of genes but please remember that the annotation packages were built a few months ago and it is thus not unusual for people to find discrepancies. One solution is to build the annotation package yourself using AnnBuilder. >X-Original-To: jzhang at jimmy.harvard.edu >Delivered-To: jzhang at jimmy.harvard.edu >X-Spam-Checker-Version: SpamAssassin 3.1.1 (2006-03-10) on hypatia.math.ethz.ch >X-Spam-Level: >X-Spam-Status: No, score=-0.1 required=5.0 tests=AWL, BAYES_50, SPF_HELO_PASS autolearn=no version=3.1.1 >X-Injected-Via-Gmane: http://gmane.org/ >To: bioconductor at stat.math.ethz.ch >From: Hilmar Berger <hilmar.berger at="" imise.uni-leipzig.de=""> >Date: Thu, 13 Jul 2006 11:54:45 +0000 (UTC) >Mime-Version: 1.0 >X-Complaints-To: usenet at sea.gmane.org >X-Gmane-NNTP-Posting-Host: main.gmane.org >User-Agent: Loom/3.14 (http://gmane.org/) >X-Loom-IP: 139.18.158.245 (Mozilla/4.0 (compatible; MSIE 6.0; Windows NT 5.0)) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Subject: [BioC] Missing chromosomal locations in hgu133a package >X-BeenThere: bioconductor at stat.math.ethz.ch >X-Mailman-Version: 2.1.8 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="unsubscribe"> >List-Archive: <https: stat.ethz.ch="" pipermail="" bioconductor=""> >List-Post: <mailto:bioconductor at="" stat.math.ethz.ch=""> >List-Help: <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="help"> >List-Subscribe: <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor="">, <mailto:bioconductor-request at="" stat.math.ethz.ch?subject="subscribe"> >Content-Transfer-Encoding: 7bit >X-PMX-Version: 5.2.0.266434, Antispam-Engine: 2.4.0.264935, Antispam- Data: 2006.7.13.45432 >X-PMX-Spam: Probability=7%, Report='__CP_URI_IN_BODY 0, __CT 0, __CTE 0, __CTYPE_CHARSET_QUOTED 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, __MIME_TEXT_ONLY 0, __MIME_VERSION 0, __SANE_MSGID 0, __STOCK_CRUFT 0, __USER_AGENT 0' > >Hi all, > >we found that there are about 8-9% of all probesets in the hgu133a package for >which no information on chromosomal location (i.e. base pairs from the >telomere) is available. >However, other public databases like Golden Path offer start and end positions >for each probeset on the array. What is the reason for this discrepancy ? > >What are the paths AnnBuilder uses in order to map probeset-IDs to chromosomal >locations ? > >Would it be safe to use chromosomal locations obtained from other sources >directly instead of relying on the hgu133a package ? > >Regards, >Hilmar > >_______________________________________________ >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 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

Hi Jianhua, thanks for Your answer. I'm aware of the fact I could create annotation packages on my own using AnnBuilder. However, the comparison I mentioned was of GoldenPath data and annotation packages of about the same date (mid 2005), and even current annotation packages show this discrepancy in the number of chromosomal locations provided in hgu133a. So I wondered if there is some good reason to not provide chromosomal locations for some probesets (e.g. unreliable mappings in GoldenPath) or if this is because of special paths AnnBuilder uses to merge all sources. Regards, Hilmar

>thanks for Your answer. I'm aware of the fact I could create annotation >packages on my own using AnnBuilder. However, the comparison I mentioned >was of GoldenPath data and annotation packages of about the same date >(mid 2005), and even current annotation packages show this discrepancy >in the number of chromosomal locations provided in hgu133a. So I >wondered if there is some good reason to not provide chromosomal >locations for some probesets (e.g. unreliable mappings in GoldenPath) or >if this is because of special paths AnnBuilder uses to merge all sources. AnnBuilder does not make any decision on who gets mapped and who does not. I will have to step through the mapping process to tell you what might be the problem. Could you give me a few of the probes that are missed again? Thanks. > >Regards, >Hilmar > >_______________________________________________ >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 Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

>>>thanks for Your answer. I'm aware of the fact I could create annotation >>>packages on my own using AnnBuilder. However, the comparison I mentioned >>>was of GoldenPath data and annotation packages of about the same date >>>(mid 2005), and even current annotation packages show this discrepancy >>>in the number of chromosomal locations provided in hgu133a. So I >>>wondered if there is some good reason to not provide chromosomal >>>locations for some probesets (e.g. unreliable mappings in GoldenPath) or >>>if this is because of special paths AnnBuilder uses to merge all sources. >> There may be two reasons. 1. AnnBuilder uses RefLink.txt and RefGene.txt from Golden Path for annotation. Location data were missing from the file for some of the genes/probes(ie. 8847/216856_s_at) in a test run. Need to talk to Golden Path about htis. 2. The base file used to build the annotation package may not be in sync with the current probe-GB mapping provided by AffyMetrix. Nianhua, do you know if a fresh download from AffyMetrix was used for release 1.8? >> >> AnnBuilder does not make any decision on who gets mapped and who does not. I >> will have to step through the mapping process to tell you what might be the >> problem. Could you give me a few of the probes that are missed again? >> >> Thanks. >> >> >> >>>Regards, >>>Hilmar >>> >>>_______________________________________________ >>>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 >> >> Jianhua Zhang >> Department of Medical Oncology >> Dana-Farber Cancer Institute >> 44 Binney Street >> Boston, MA 02115-6084 >> > >-- > >Hilmar Berger >Studienkoordinator >Institut f?r medizinische Informatik, Statistik und Epidemiologie >Universit?t Leipzig >H?rtelstr. 16-18 >D-04107 Leipzig > >Tel. +49 341 97 16 101 >Fax. +49 341 97 16 109 >email: hilmar.berger at imise.uni-leipzig.de Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

> 2. The base file used to build the annotation package may not be in sync with > the current probe-GB mapping provided by AffyMetrix. Nianhua, do you know if a > fresh download from AffyMetrix was used for release 1.8? > The probe-GB mapping from Affymetrix that was used for release 1.8 was dated Dec. 19, 2005. Six files were used to get unified probe to Entrez Gene mapping: 1. probe-GB mapping from Affymetrix 2. probe-UniGene mapping from Affymetrix 3. probe-Entrez Gene mapping from Affymetrix 4. probe-Entrez Gene mapping from DCHIP 5. probe-Entrez Gene mapping from U. Michigan 6. probe-Entrez Gene mapping from another source (EA) 1 is the primary source, and 2-6 are supplimental sources. 1-3 are all dated Dec 19, 2005. 4-6 are pretty old files (>1 years old). thanks nianhua