Hi, Is there a utility in BioC to retrieve data sets in NCBI GEO? Will the EFetch in Entrez do the job? Parsing something like this is not a big deal, but I would like to have a cup of coffee instead. Thanks! -Simon http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?view=data&acc=G SM79114

Have a look at queryGEO of AnnBuilder. >X-Original-To: jzhang at jimmy.harvard.edu >Delivered-To: jzhang at jimmy.harvard.edu >X-Spam-Checker-Version: SpamAssassin 3.1.0 (2005-09-13) on hypatia.math.ethz.ch >X-Spam-Level: >X-Spam-Status: No, score=0.1 required=5.0 tests=AWL, BAYES_50 autolearn=no version=3.1.0 >From: "Simon Lin" <simon.lin at="" duke.edu=""> >To: <bioconductor at="" stat.math.ethz.ch=""> >Date: Thu, 22 Dec 2005 11:21:08 -0600 >MIME-Version: 1.0 >X-Priority: 3 >X-MSMail-Priority: Normal >X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2900.2527 >Received-SPF: pass hypatia.math.ethz.ch: 129.132.145.15 is authenticated by a trusted mechanism) >Received-SPF: none (hypatia: domain of simon.lin at duke.edu does not designate permitted sender hosts) >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Subject: [BioC] Retrieving microarray data from GEO? >X-BeenThere: bioconductor at stat.math.ethz.ch >X-Mailman-Version: 2.1.6 >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: 4.7.1.128075, Antispam-Engine: 2.1.0.0, Antispam-Data: 2005.12.22.16 >X-PMX-Spam: Probability=7%, Report='__CT 0, __CTE 0, __CTYPE_CHARSET_QUOTED 0, __CT_TEXT_PLAIN 0, __HAS_MSGID 0, __HAS_MSMAIL_PRI 0, __HAS_X_MAILER 0, __HAS_X_PRIORITY 0, __MIME_TEXT_ONLY 0, __MIME_VERSION 0, __SANE_MSGID 0, __STOCK_CRUFT 0' > >Hi, Is there a utility in BioC to retrieve data sets in NCBI GEO? Will the >EFetch in Entrez do the job? Parsing something like this is not a big deal, >but I would like to have a cup of coffee instead. Thanks! -Simon >http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?view=data&acc= GSM79114 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084