[BioC] Missing chromosomal locations in hgu133a package

John Zhang jzhang at jimmy.harvard.edu
Thu Jul 13 14:43:45 CEST 2006

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-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: (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:, Antispam-Engine:, Antispam-Data: 
>X-PMX-Spam: Probability=7%, Report='__CP_URI_IN_BODY 0, __CT 0, __CTE 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 ?
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>Search the archives: 

Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084

More information about the Bioconductor mailing list