hi every one I have just started working with data coming from RNA-seq.I have run an edgeR program on the the data in linux,for differential expression ,but in one of the steps I got the error like this: cls <- gsub("[0-9]", "", colnames(dataList$data)) > cls character(0) and after this I will get error in next steps.I want to know if any one has got an error like this?if yes how to solve it? Med venlig hilsen Leila Farajzadeh Ph.d. studerende AARHUS UNIVERSITET Det Jordbrugsvidenskabelige Fakultet Inst. for Genetik og Bioteknologi Blichers Allé 20, Postboks 50 8830 Tjele Telefon: 8999 1900 Direkte: 8999 1353 E-mail: Leila.Farajzadeh@agrsci.dk<mailto:leila.farajzadeh@agrsci.dk> Web: www.agrsci.dk<http: www.agrsci.dk=""/> ________________________________ DJF udbyder nye uddannelser<http: www.agrsci.dk="" ny_navigation="" uddannelse=""/>. Tilmeld dig DJF's nyhedsbrev<http: www.agrsci.dk="" user="" register?lan="dan-DK">. Denne email kan indeholde fortrolig information. Enhver brug eller offentliggørelse af denne email uden skriftlig tilladelse fra DJF er ikke tilladt. Hvis De ikke er den tiltænkte adressat, bedes De venligst straks underrette DJF samt slette emailen. [[alternative HTML version deleted]]

Hi Leila, this isn't an error as such - R is doing exactly what you're asking it to do. With gsub, you're currently searching for colnames containing a number (the first "[0-9]" argument), and you're replacing those with nothing (the second "" argument). Try having a look at the help pages for gsub, or send us for example the output of colnames(dataList$data) and tell us how you want these column names to be changed. You'll probably want to include part of your search pattern in (), and use that for replacement with \\1. Cheers \Heidi > hi every one > I have just started working with data coming from RNA-seq.I have run an > edgeR program on the the data in linux,for differential expression ,but in > one of the steps I got the error like this: > > cls <- gsub("[0-9]", "", colnames(dataList$data)) >> cls > character(0) > > and after this I will get error in next steps.I want to know if any one > has got an error like this?if yes how to solve it? > > > Med venlig hilsen > > Leila Farajzadeh > Ph.d. studerende > > > > AARHUS UNIVERSITET > Det Jordbrugsvidenskabelige Fakultet > Inst. for Genetik og Bioteknologi > Blichers All? 20, Postboks 50 > 8830 Tjele > > Telefon: 8999 1900 > Direkte: 8999 1353 > E-mail: Leila.Farajzadeh at agrsci.dk<mailto:leila.farajzadeh at="" agrsci.dk=""> > Web: www.agrsci.dk<http: www.agrsci.dk=""/> > > ________________________________ > DJF udbyder nye > uddannelser<http: www.agrsci.dk="" ny_navigation="" uddannelse=""/>. > > Tilmeld dig DJF's > nyhedsbrev<http: www.agrsci.dk="" user="" register?lan="dan-DK">. > > Denne email kan indeholde fortrolig information. Enhver brug eller > offentligg?relse af denne email uden skriftlig tilladelse fra DJF er ikke > tilladt. Hvis De ikke er den tilt?nkte adressat, bedes De venligst straks > underrette DJF samt slette emailen. > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

Dear list, I am trying to find function enrichment for a gene list that we have obtained through chip-chip experiments. The chip that we have used is the Agilent human promoter array, which consists of two differents slides. I cannot find any package corresponding to the annotation of this chip, which I think I need to obtain "gene universe" information and, from there, obtain gene set enrichments using GO. Does an annotation package for that chip exists or should I build the annotation package myself, and if so, could you provide pointers to how to build it? Thanks in advance Marc -- ----------------------------------------------------- Marc Noguera i Julian, PhD Genomics unit / Bioinformatics Institut de Medicina Preventiva i Personalitzada del C?ncer (IMPPC) B-10 Office Carretera de Can Ruti Cam? de les Escoles s/n 08916 Badalona, Barcelona

Dear J Zhang, I'm a PhD student. I was looking for a package that provides functions to identify minimum common genomic regions of interests based on segmented copy number data from multiple samples. I've found yours could be very useful for me. Your Manual shows how to generate the segment data based on raw data using DNAcopy package, and then, use these segment data (as a DNAcopy class object) as the input to the cghMCR function. My problem is I've generated the segment list using other method. This segment list has the same parameters than the segment list you use as example (called "segData") but it is a data frame object, not a DNAcopy object like "segData". How could I apply cghMCR and MCR functions using my R data frame? There is some method to get a DNAcopy class object from my segment list? Thanks Luz G Alonso lgarcia at cipf.es PhD Student Bioinformatics and Genomics Department Centro de Investigaciones Principe Felipe Avda. Autopista Saler 16, 46012 Valencia, Spain Phone: +34 96 328 96 80 Fax: +34 96 328 97 01 http://bioinfo.cipf.es/

Luz, There is a better way of finding commonly altered regions/genes across samples using the CNTools and cghMCR packages. Please read the vignettes of the two packages in the release (2.5) or devel track. The tools do take the segment list of CBS as the input. JZ >X-Original-To: jzhang at jimmy.harvard.edu >Delivered-To: jzhang at jimmy.harvard.edu >X-IronPort-Anti-Spam-Filtered: true >X-IronPort-Anti-Spam-Result: AogAAHbiTkuBhJEPkWdsb2JhbACbdwEBAQEJCwoHEwW8awKCKIIGBIkw >X-IronPort-AV: E=Sophos;i="4.49,275,1262581200"; d="scan'208";a="144986670" >X-SBRS: 4.5 >X-Spam-Checker-Version: SpamAssassin 3.2.5 (2008-06-10) on hypatia.math.ethz.ch >X-Spam-Level: >X-Spam-Status: No, score=-4.8 required=5.0 tests=BAYES_00, MISSING_SUBJECT, RCVD_IN_DNSWL_MED autolearn=ham version=3.2.5 >X-IronPort-Anti-Spam-Filtered: true >X-IronPort-Anti-Spam-Result: Ah0CAPIsTEusEGcz/2dsb2JhbAAIg1eWY64JjV0CgSl/gTBWBIkq >X-IronPort-AV: E=Sophos;i="4.49,262,1262559600"; d="scan'208";a="97510715" >From: Luz G Alonso <lgarcia at="" cipf.es=""> >To: bioconductor at stat.math.ethz.ch >Date: Tue, 12 Jan 2010 17:10:56 +0100 >User-Agent: KMail/1.9.10 >MIME-Version: 1.0 >Content-Disposition: inline >X-Tag-Only: YES >X-Filter-Node: phil1.ethz.ch >X-USF-Spam-Level: -- >X-USF-Spam-Status: hits=-2.3 tests=BAYES_00,MISSING_SUBJECT >X-USF-Spam-Flag: NO >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >X-Mailman-Approved-At: Thu, 14 Jan 2010 18:25:29 +0100 >Subject: [BioC] (no subject) >X-BeenThere: bioconductor at stat.math.ethz.ch >X-Mailman-Version: 2.1.13 >List-Id: The Bioconductor Project Mailing List <bioconductor.stat.math.ethz.ch> >List-Unsubscribe: <https: stat.ethz.ch="" mailman="" options="" 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 > > >Dear J Zhang, >I'm a PhD student. >I was looking for a package that provides functions to identify minimum common >genomic regions of interests based on segmented copy number data from >multiple samples. I've found yours could be very useful for me. >Your Manual shows how to generate the segment data based on raw data using >DNAcopy package, and then, use these segment data (as a DNAcopy class object) >as the input to the cghMCR function. My problem is I've generated the segment >list using other method. This segment list has the same parameters than the >segment list you use as example (called "segData") but it is a data frame >object, not a DNAcopy object like "segData". >How could I apply cghMCR and MCR functions using my R data frame? There is >some method to get a DNAcopy class object from my segment list? > >Thanks > > > >Luz G Alonso lgarcia at cipf.es >PhD Student >Bioinformatics and Genomics Department >Centro de Investigaciones Principe Felipe >Avda. Autopista Saler 16, >46012 Valencia, Spain >Phone: +34 96 328 96 80 >Fax: +34 96 328 97 01 >http://bioinfo.cipf.es/ > >_______________________________________________ >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