[BioC] affymetrix pig annotation data

[John Zhang]

I do not think AnnBuilder has been configured/tested for handling pig chip 
annotation yet. The functions should work for human, mouse, and rat but may not 
work for other organisms.


>X-Original-To: jzhang at jimmy.harvard.edu
>Delivered-To: jzhang at jimmy.harvard.edu
>Date: Mon, 14 Nov 2005 18:28:32 +0100
>From: Morten Mattingsdal <morten.mattingsdal at student.uib.no>
>User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206)
>X-Accept-Language: en-us, en
>MIME-Version: 1.0
>To: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
>X-UiO-Spam-info: not spam, SpamAssassin (score=-2.279, required 12, 
autolearn=disabled, AWL -2.28, MISSING_SUBJECT 0.00)
>Received-SPF: pass (hypatia.math.ethz.ch: 129.132.145.15 is authenticated by a 
trusted mechanism)
>Received-SPF: none (hypatia: domain of morten.mattingsdal at student.uib.no does 
not designate permitted sender hosts)
>X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch
>Subject: [BioC] affymetrix pig annotation data
>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: quoted-printable
>X-PMX-Version: 4.7.1.128075, Antispam-Engine: 2.1.0.0, Antispam-Data: 
2005.11.14.17
>X-PMX-Spam: Probability=7%, Report='__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'
>X-Spam-Checker-Version: SpamAssassin 3.0.1 (2004-10-22) on  
pascal.dfci.harvard.edu
>X-Spam-Level: 
>X-Spam-Status: No, score=-2.5 required=3.0 tests=AWL,BAYES_00, 
TO_ADDRESS_EQ_REAL autolearn=no version=3.0.1
>
>Hello open-source spirits,
>
>Im trying to build an annotation data library for the Sus scrofa (common 
>pig) affymetrix chip: GeneChip® Porcine Genome Array
>http://www.affymetrix.com/products/arrays/specific/porcine.affx
>
>but Im not very sucessful in doing so.. my error is
>
>Error in "baseFile<-"(`*tmp*`, value = 
>"C:\\DOCUME~1\\mortema\\LOCALS~1\\Temp\\Rtmp2376\\tempFile26288") :
>        no direct or inherited method for function 'baseFile<-' for this 
>call
>
>and I dont know what this is trying so tell me. My imput is probe ID in 
>coloum 1 and genbank acc.nr in coloum 2.
>"Ssc.11.1.S1_at"    "NM_213802.1"
>and I have succesfully build packages before with human and mouse. But 
>this is my first go at pig.
>
>Does anyone have this library already build or can someone help me build 
>it ?
>
>(im deeply sorry if this is already listed in the metadata dir at 
>bioconductor. But cant find anything related to pig)
>
>best
>morten
>
>_______________________________________________
>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