Dear all,

I have a general question concerning the use of DNAcopy with high density SNP/CN arrays. If I understand correctly (which certainly might 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 imagine that the default values should be somehow modified, especially those for the "segment" function. Are, in your experience, the default settings OK for the SNP6.0 platform or would you recommend different values for the main parameters (segment undoing, trimming etc)?

Many thanks!