Question: Calling genes present or absent in CGH data
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gravatar for adam_pgsql
9.5 years ago by
adam_pgsql70
adam_pgsql70 wrote:
Hi, I have a CGH data set (two colour spotted array data) where i have performed various filtering and normalisation steps using LIMMA. I now have a matrix of log ratios and was wondering which are people's preferred functions or tools to call genes as present or absent? thanks for any advice Adam
cgh limma • 618 views
ADD COMMENTlink modified 9.5 years ago by Sean Davis21k • written 9.5 years ago by adam_pgsql70
Answer: Calling genes present or absent in CGH data
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gravatar for John Zhang
9.5 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
You may want to try the segment function of DNAcopy to identify regions with gains or losses. If you then would like to identify regions whowing gains/losses across samples, look at packages like CNTools, cghMCR, CGHcall, and CGHregions. >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: AmoAAJ83WUuBhJEPkWdsb2JhbACBRZpiAQEBAQkLCgcTBbt2hDwE >X-IronPort-AV: E=Sophos;i="4.49,324,1262581200"; d="scan'208";a="146786654" >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=-4.6 required=5.0 tests=AWL, BAYES_00, RCVD_IN_DNSWL_MED autolearn=ham version=3.2.5 >Mime-Version: 1.0 (Apple Message framework v1077) >X-Mailtags-Uuid: 9957FA95-FEA0-4267-B955-E917C15C1F2C >From: adam_pgsql <adam_pgsql at="" witneyweb.org=""> >X-Mailtags-Timestamp: 2010-01-22 13:28:23 +0000 >Date: Fri, 22 Jan 2010 13:28:23 +0000 >X-Mailtags-Version: 2.5 >To: BioConductor List <bioconductor at="" stat.math.ethz.ch=""> >X-SGUL-MailScanner-Information: Please contact the ISP for more information >X-SGUL-MailScanner-ID: 1NYJYm-0005no-8I >X-SGUL-MailScanner-MH1: Found to be clean >X-SGUL-MailScanner-SpamCheck: not spam, SpamAssassin (not cached, score=-4.399, required 5, autolearn=not spam, ALL_TRUSTED -1.80, BAYES_00 -2.60) >X-SGUL-MailScanner-From: adam_pgsql at witneyweb.org >X-USF-Spam-Status: No >X-Tag-Only: YES >X-Filter-Node: phil3.ethz.ch >X-USF-Spam-Level: -- >X-USF-Spam-Status: hits=-2.5 tests=BAYES_00,FORGED_RCVD_HELO >X-USF-Spam-Flag: NO >X-Virus-Scanned: by amavisd-new at stat.math.ethz.ch >Subject: [BioC] Calling genes present or absent in CGH data >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 > >Hi, > >I have a CGH data set (two colour spotted array data) where i have performed various filtering and normalisation steps using LIMMA. I now have a matrix of log ratios and was wondering which are people's preferred functions or tools to call genes as present or absent? > >thanks for any advice > >Adam > >_______________________________________________ >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
Answer: Calling genes present or absent in CGH data
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gravatar for Sean Davis
9.5 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Fri, Jan 22, 2010 at 8:28 AM, adam_pgsql <adam_pgsql at="" witneyweb.org=""> wrote: > Hi, > > I have a CGH data set (two colour spotted array data) where i have performed various filtering and normalisation steps using LIMMA. I now have a matrix of log ratios and was wondering which are people's preferred functions or tools to call genes as present or absent? > Hi, Adam. CGH data are generally treated somewhat differently than gene expression and so a different set of tools is often used. You might look at any of a dozen or so methods related to CGH segmentation. There is a literature comparing various methods, also. For starters, you might look here: http://bioconductor.org/packages/release/CopyNumberVariants.html For literature, consider checking out this as a "review": http://www.ncbi.nlm.nih.gov/pubmed/16081473 And for an interesting approach to comparison between methods, see: http://www.ncbi.nlm.nih.gov/pubmed/18296463 Sean
ADD COMMENTlink written 9.5 years ago by Sean Davis21k
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