Figure 6

A comparison of genome-wide copy number estimates using four variants of the OncoSNP model. Heatmaps are shown for genome-wide copy numbers from four variants of our model: (i) Germline model involving no Log R Ratio baseline correction or normal contamination, (ii) Ploidy-only model estimation of baseline correction used, (iii) Normal-only model estimation of normal DNA contamination used and (iv) Full model the complete OncoSNP model incorporating both baseline and normal DNA contamination estimation. The full model is able to accurately reproduce the same copy number profile for both cell lines (SW837/SW403) even in the presence of increasing levels of normal DNA contamination. If normal contamination or baseline correction estimation is not used incorrect copy number profiles maybe given.