I have a question concerning the use of DNAcopy on high density SNP/CN arrays. If I understand correctly (which might well not be the case), the default settings of DNAcopy were chosen to work well with low density CGH arrays. However in the case of high density arrays like the Affymetrix SNP6.0, I would expect these settings to be inadequate, especially for the "segment" function. Are, in your experience, such settings OK for the SNP6.0 platform or would you recommend different values for the main parameters (segment undoing, trimming etc)?
Thanks a lot!