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.