Dear Vincent, Spot on. Many Thanks. Works fine now. Wondering if at all there is a way to create genome plots per sample (23 plots per chromosome) but showing gains and losses per sample through all chromosomes ? Many Thanks, --E From: Vincent Carey [mailto:stvjc@channing.harvard.edu] Sent: 30 March 2012 17:56 To: Ekta Jain Cc: bioconductor@r-project.org Subject: Re: [BioC] DNAcopy for CNV in SNP Affy 6.0 Somewhat unlikely that you will get much help using an R 2.9.1 -- please upgrade to 2.14.1, install with biocLite, and try again. On Fri, Mar 30, 2012 at 8:14 AM, Ekta Jain <ekta_jain@jubilantbiosys.com<mailto:ekta_jain@jubilantbiosys.com>> wrote: Dear All, I am trying to use the DNAcopy package to perform CBS segmentation on my copy number data. As given in the manual, i have created my CNA.object by reading a file for chromosome, position and values for one sample. When performing smoothed.CNA.object <- smooth.CNA(CNA.object) I get the following error: > smoothed.CNA.object <- smooth.CNA(CNA.Object) Error in if (xi > max(xnbhd) + oSD) xi <- median(c(xi, xnbhd)) + sSD : missing value where TRUE/FALSE needed In addition: Warning message: In max(xnbhd) : no non-missing arguments to max; returning -Inf I will highly appreciate if someone can tell me where could i be possibly going wrong? Thanks and Regards, Ekta > sessionInfo() R version 2.9.1 (2009-06-26) i386-pc-mingw32 locale: LC_COLLATE=English_India.1252;LC_CTYPE=English_India.1252;LC_MONETARY= English_India.1252;LC_NUMERIC=C;LC_TIME=English_India.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.18.3 affy_1.22.1 Biobase_2.4.1 GLAD_2.0.0 DNAcopy_1.18.0 loaded via a namespace (and not attached): [1] affyio_1.12.0 preprocessCore_1.6.0 tools_2.9.1 The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, a! nd is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com<http: www.jubl.com=""> [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@r-project.org<mailto:bioconductor@r-project.org> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com [[alternative HTML version deleted]]

Dear BioC Help, I am having issues with the CGHcall package when using in R. I first employ DNAcopy package to smooth and segment my data (CNA.object) and get an error while performing post normalize processing using the CGHcall package. > smoothed.CNA.object <- smooth.CNA(CNA.object) > segment.smoothed.CNA.object <- segment(smoothed.CNA.object, verbose=1) Analyzing: ABC1 Analyzing: BEN > postseg.cghdata <- postsegnormalize(segment.smoothed.CNA.object) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "segmented", for signature "DNAcopy" Is there any structural difference between CNA object and CGH object type? Please do let me know where i could possibly be going wrong. Thank you, Ekta > sessionInfo() R version 2.14.1 (2011-12-22) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_India.1252 LC_CTYPE=English_India.1252 [3] LC_MONETARY=English_India.1252 LC_NUMERIC=C [5] LC_TIME=English_India.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] CGHcall_2.14.0 CGHbase_1.12.0 marray_1.34.0 [4] limma_3.10.3 Biobase_2.14.0 impute_1.28.0 [7] DNAcopy_1.28.0 BiocInstaller_1.2.1 loaded via a namespace (and not attached): [1] tools_2.14.1 The information contained in this electronic message and in any attachments to this message is confidential, legally privileged and intended only for use by the person or entity to which this electronic message is addressed. If you are not the intended recipient, and have received this message in error, please notify the sender and system manager by return email and delete the message and its attachments and also you are hereby notified that any distribution, copying, review, retransmission, dissemination or other use of this electronic transmission or the information contained in it is strictly prohibited. Please note that any views or opinions presented in this email are solely those of the author and may not represent those of the Company or bind the Company. Any commitments made over e-mail are not financially binding on the company unless accompanied or followed by a valid purchase order. This message has been scanned for viruses and dangerous content by Mail Scanner, and is believed to be clean. The Company accepts no liability for any damage caused by any virus transmitted by this email. www.jubl.com