CGHcall error
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James Morris ▴ 40
@james-morris-2002
Last seen 6.8 years ago
Hello, I have been using CGHcall to analyse our aCGH experiments for the past 6 months and it has been working great (mac os x 10.4, R 2.7.0) However we recently got a new server (mac os x 10.5) and on to it I installed the latest version of R 2.7.2 and CGHcall, but now CGHcall no longer works! It gives the following error: Skipping normalization ... Smoothing outliers ... Error in function (classes, fdef, mtable) : Unable to find an inherited method for function "copynumber", for signature "data.frame" Calls: normalize ... inherits -> <anonymous> -> copynumber -> <anonymous> Execution halted Any help would be great Thank you, James Morris Gynaecological Cancer Research Laboratories, UCL EGA Institute for Women's Health, University College London, Paul O'Gorman Building, 72 Huntley Street, London WC1E 6DD United Kingdom Telephone: 020 3108 2002 [[alternative HTML version deleted]]
aCGH Normalization Cancer aCGH CGHcall copynumber aCGH Normalization Cancer aCGH CGHcall • 590 views
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@sean-davis-490
Last seen 15 days ago
United States
On Fri, Oct 3, 2008 at 9:45 AM, James Morris <james.morris at="" ucl.ac.uk=""> wrote: > Hello, > > > > I have been using CGHcall to analyse our aCGH experiments for the past 6 > months and it has been working great (mac os x 10.4, R 2.7.0) > > > > However we recently got a new server (mac os x 10.5) and on to it I > installed the latest version of R 2.7.2 and CGHcall, but now CGHcall no > longer works! > > > > It gives the following error: > > > > Skipping normalization ... > > Smoothing outliers ... > > Error in function (classes, fdef, mtable) : > > Unable to find an inherited method for function "copynumber", for > signature "data.frame" Hi, James. You'll probably need to post the code that you have used along with sessionInfo(). Sean
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Daniel Rico ▴ 110
@daniel-rico-2390
Last seen 6.8 years ago
Hi James, Check the new vignette from the latest BioConductor version: now you must create and work with CGHcall objects, as the new version does not support data.frames directly (but there is a function that takes the data.frame with raw data and converts it to the corresponding CGHcall package). Daniel On Oct 3, 2008, at 3:45 PM, James Morris wrote: > Hello, > > > > I have been using CGHcall to analyse our aCGH experiments for the > past 6 > months and it has been working great (mac os x 10.4, R 2.7.0) > > > > However we recently got a new server (mac os x 10.5) and on to it I > installed the latest version of R 2.7.2 and CGHcall, but now CGHcall > no > longer works! > > > > It gives the following error: > > > > Skipping normalization ... > > Smoothing outliers ... > > Error in function (classes, fdef, mtable) : > > Unable to find an inherited method for function "copynumber", for > signature "data.frame" > > Calls: normalize ... inherits -> <anonymous> -> copynumber -> > <anonymous> > > Execution halted > > > > Any help would be great > > > > Thank you, > > > > James Morris > > > > Gynaecological Cancer Research Laboratories, > > UCL EGA Institute for Women's Health, > > University College London, > > Paul O'Gorman Building, > > 72 Huntley Street, > > London WC1E 6DD > > United Kingdom > > > > Telephone: 020 3108 2002 > > > [[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 ******************************************** Daniel Rico Rodriguez, PhD. Structural Computational Biology Group & Bioinformatics Unit Spanish National Cancer Research Center, CNIO Melchor Fernandez Almagro, 3. 28029 Madrid, Spain. Phone: +34 91 224 69 00 #3062 drico at cnio.es http://www.cnio.es ******************************************** **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y ...{{dropped:3}}
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