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gravatar for Leila Farajzadeh
9.5 years ago by
Leila Farajzadeh10 wrote:
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$data)) > cls character(0) and after this I will get error in next steps.I want to know if any one has got an error like this?if yes how to solve it? Med venlig hilsen Leila Farajzadeh Ph.d. studerende AARHUS UNIVERSITET Det Jordbrugsvidenskabelige Fakultet Inst. for Genetik og Bioteknologi Blichers Allé 20, Postboks 50 8830 Tjele Telefon: 8999 1900 Direkte: 8999 1353 E-mail: Leila.Farajzadeh@agrsci.dk<mailto:leila.farajzadeh@agrsci.dk> Web: www.agrsci.dk<http: www.agrsci.dk=""/> ________________________________ DJF udbyder nye uddannelser<http: www.agrsci.dk="" ny_navigation="" uddannelse=""/>. Tilmeld dig DJF's nyhedsbrev<http: www.agrsci.dk="" user="" register?lan="dan-DK">. Denne email kan indeholde fortrolig information. Enhver brug eller offentliggørelse af denne email uden skriftlig tilladelse fra DJF er ikke tilladt. Hvis De ikke er den tiltænkte adressat, bedes De venligst straks underrette DJF samt slette emailen. [[alternative HTML version deleted]]
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ADD COMMENTlink modified 9.5 years ago by John Zhang2.9k • written 9.5 years ago by Leila Farajzadeh10
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gravatar for Heidi Dvinge
9.5 years ago by
Heidi Dvinge2.0k
Heidi Dvinge2.0k wrote:
Hi Leila, this isn't an error as such - R is doing exactly what you're asking it to do. With gsub, you're currently searching for colnames containing a number (the first "[0-9]" argument), and you're replacing those with nothing (the second "" argument). Try having a look at the help pages for gsub, or send us for example the output of colnames(dataList$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
ADD COMMENTlink written 9.5 years ago by Heidi Dvinge2.0k
Answer: (no subject)
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gravatar for Marc Noguera
9.5 years ago by
Marc Noguera100
Marc Noguera100 wrote:
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
ADD COMMENTlink written 9.5 years ago by Marc Noguera100
On Mon, Jan 11, 2010 at 7:15 AM, Marc Noguera <mnoguera at="" imppc.org=""> wrote: > 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? Hi, Marc. The chip annotation packages will not be helpful for this situation, as they are gene-based. Your chips are not gene-based, so an annotation package built for them, even if you could get it built, probably wouldn't make a lot of sense. Instead, you will probably need to generate a gene list of all genes covered by the array and then a gene list of the genes showing promoter signal. With those two lists, you should be able to define your universe and use the org.Hs.eg.db package for GO enrichment. Sean
ADD REPLYlink written 9.5 years ago by Sean Davis21k
Thanks for the help Sean, It has been very useful. I have managed to create the geneUniverse from chip data and run the hyperGTests on my selected genesets looking for enrichment. Now I have hyperGResults instances as a result, and apart from summary information on MF, BP or CC with the corresponding p-values I would like to know how could I run some kind of FDR corrections on these results. Also, what are the available tools for visualizing such data. I am checking topGO now, but maybe there are some other tools. Thanks in advance Marc Sean Davis wrote: > On Mon, Jan 11, 2010 at 7:15 AM, Marc Noguera <mnoguera at="" imppc.org=""> wrote: > >> 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? >> > > Hi, Marc. The chip annotation packages will not be helpful for this > situation, as they are gene-based. Your chips are not gene-based, so > an annotation package built for them, even if you could get it built, > probably wouldn't make a lot of sense. Instead, you will probably > need to generate a gene list of all genes covered by the array and > then a gene list of the genes showing promoter signal. With those two > lists, you should be able to define your universe and use the > org.Hs.eg.db package for GO enrichment. > > Sean > -- ----------------------------------------------------- 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
ADD REPLYlink written 9.5 years ago by Marc Noguera100
On Tue, Jan 12, 2010 at 4:26 AM, Marc Noguera <mnoguera at="" imppc.org=""> wrote: > Thanks for the help Sean, It has been very useful. > I have managed to create the geneUniverse from chip data and run the > hyperGTests on my selected genesets looking for enrichment. > Now I have hyperGResults instances as a result, and apart from summary > information on MF, BP or CC with the corresponding p-values I would like > to know how could I run some kind of FDR corrections on these results. The correct statistical treatment of nested categories is probably still a topic of research. However, our own Seth Falcon and Robert Gentleman (among others) have looked into this: http://www.ncbi.nlm.nih.gov/pubmed/17098774 > Also, what are the available tools for visualizing such data. I am > checking topGO now, but maybe there are some other tools. I'm not sure what you mean by "visualizing", but take a look at the Rgraphviz package. Sean > Marc > Sean Davis wrote: >> On Mon, Jan 11, 2010 at 7:15 AM, Marc Noguera <mnoguera at="" imppc.org=""> wrote: >> >>> 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? >>> >> >> Hi, Marc. ?The chip annotation packages will not be helpful for this >> situation, as they are gene-based. ?Your chips are not gene-based, so >> an annotation package built for them, even if you could get it built, >> probably wouldn't make a lot of sense. ?Instead, you will probably >> need to generate a gene list of all genes covered by the array and >> then a gene list of the genes showing promoter signal. ?With those two >> lists, you should be able to define your universe and use the >> org.Hs.eg.db package for GO enrichment. >> >> Sean >> > > > -- > ----------------------------------------------------- > 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 > ------------------------------------------------------- > >
ADD REPLYlink written 9.5 years ago by Sean Davis21k
Answer: (no subject)
0
gravatar for Luz G Alonso
9.5 years ago by
Luz G Alonso20
Luz G Alonso20 wrote:
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/
ADD COMMENTlink written 9.5 years ago by Luz G Alonso20
Answer: (no subject)
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gravatar for John Zhang
9.5 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
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
ADD COMMENTlink written 9.5 years ago by John Zhang2.9k
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