HI, I am using DNAcopy in order to plots my agilent CGHarrays (mouse) I have done the segmentation using the segment () function and now I want to plot my data using plot(). I know that chromosome 15 is duplicated in my samples. -With this configuration plot type=w ( plot all the genome) plot(segData, plot.type="w") , the chromosomes alternate in different colours and the duplicated chromosomes are not in the right place ( it says chro7 is duplicated and I know it should be 15) -Interestingly when I plot per chromosome using the plot.type=s ,I don't have this problem and chromsome 15 is duplicated. I don't understand :( any idea ? thanks Nat -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

Dear Nat I don't know this package in any detail, and other people will have more specific insights, but I think chances of someone being able to help you will increase if you - post a small, self-contained, reproducible example - provide the output of sessionInfo(). Best wishes Wolfgang nac scripsit 05/18/2011 11:02 PM: > HI, > I am using DNAcopy in order to plots my agilent CGHarrays (mouse) > I have done the segmentation using the segment () function and now I > want to plot my data using plot(). I know that chromosome 15 is > duplicated in my samples. > -With this configuration plot type=w ( plot all the genome) > plot(segData, plot.type="w") , the chromosomes alternate in different > colours and the duplicated chromosomes are not in the right place ( it > says chro7 is duplicated and I know it should be 15) > -Interestingly when I plot per chromosome using the plot.type=s ,I don't > have this problem and chromsome 15 is duplicated. > I don't understand :( any idea ? > thanks > Nat > > > > -- Wolfgang Huber EMBL http://www.embl.de/research/units/genome_biology/huber