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Question: DNAcopy for CNV in SNP Affy 6.0
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gravatar for Ekta Jain
5.6 years ago by
Ekta Jain370
Ekta Jain370 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, 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]]
ADD COMMENTlink modified 5.6 years ago by Vincent J. Carey, Jr.6.2k • written 5.6 years ago by Ekta Jain370
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gravatar for Vincent J. Carey, Jr.
5.6 years ago by
United States
Vincent J. Carey, Jr.6.2k wrote:
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>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_MONETAR Y=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 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 5.6 years ago by Vincent J. Carey, Jr.6.2k
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