These nine panels show comparisons among CARAT, dCHIP and CNAG qPCR results of 69 autosomal SNPs from the human breast cancer cell line SK-BR-3. In each scatter plot the x-axis is the copy number derived from QPCR and the y-axis is the copy number derived from one of the three algorithms. ΔCt denotes the difference between the normal DNA sample versus SK-BR-3. The threshold cycle (Ct) is the cycle number at which the reporter fluorescence passes a fixed threshold above baseline. A positive ΔCt suggests an amplification while a negative ΔCt suggests a deletion. The copy number of SK-BR-3 based on QPCR is inferred as 2(ΔCt + 1). The red points are the 55 SNPs that were included in the CNAG analysis; the black points are the 14 additional SNPs that were included in dCHIP and CARAT analysis but were excluded from CNAG. Correlations are calculated for each of these two different SNP sets. The blue line in each panel represents the Y = X line. Panels (a), (b), and (c) compare single point analysis across the three methods; panels (d), (e), and (f) compare smoothing across neighboring points; panels (g), (h), and (i) compare genome partitioning across the three methods.