Figure 10

Example of segmentation of data after alternative normalization methods. Segmented copy number profile of chromosome 4 from smoothed (50 kBp) Agilent data for the sample from figure 7 with superimposed adaptive thresholds (± 0.171). Three different segments are highlighted with colored arrows in each panel to exemplify regions with different copy number level (a) Segmentation applied after Lowess. M values for selected segments; blue arrow 0.16, red arrow 1.02, and green arrow -0.36. (b) Segmentation applied after popLowess. M values for selected segments; blue arrow -0.07, red arrow 0.94, and green arrow -0.64.(c) Segmentation applied after Lowess normalization subsequently followed by centralization of data on median M of an individual population. M values for selected segments; blue arrow -0.05, red arrow 0.81, and green arrow -0.57.