ROC comparison with scaled data (Ovarian dataset, sample GSM492511_IC318T, hybridized to GenomeWideSNP 6.0 array). We have used the region where there is a change from 3 to 2 copies, in the begining of chromosome 1, that appears in Figure13. For the analysis, we have included the SNPs that surrounds the copy number change (specifically from 60 to 85 Mb). The SNPs within a safety zone from 70 Mb to 75 Mb are not considered in the analysis. The SNPs located upstream the change point are considered to have total CNs larger than the SNPs downstream the change point. For this particular sample (in the studied jump), NSA (with BER) differentiates better than NSA (without BER) and CalMaTe using control samples as references (MCS).