Unmatching between CBS merging resutls and pdf made by DNAcopy.plot using Varscan2 copyCaller

Question

[lee.jingu0626]

Hi everyone.

I have some questions about DNAcopy.plot.

1. After making pdf file by using DNAcopy.plot, I wanted to compare this pdf file with merging CBS segments results. When I selected some regions that indicated large-scale deletion, I guessed that the same regions in the pdf also showed same results(large-scale). But, it didn't show the results that I want.

   I think that I have a mistake about fixing the scope such as row scope(chromosome). For example, if the chromosome region is in 1~10 rows, I have to fix the scope like [1:10]. In this step, I have some mistake to choose index.

   Or are there any other problems that you can guess?

2. I want to know about removing noise in plot graph.

Thanks a lot