[BioC] Missing chromosomal locations in hgu133a package

[John Zhang]

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