Figure 1.

Overview of the proposed CNV detection algorithm. ÇOKGEN first extracts the intensity values from the Affymetrix .CEL files. It then obtains the raw copy numbers for each marker using regression with the help of the Affymetrix software's SNP genotype calls. The edge detection determines the candidate loss/gain regions from smoothed copy number signal, which is obtained by low-pass filtering the raw copy numbers. We determine the final class assignments using objective function optimization. The function is optimized using an iterative simulated annealing procedure, with initialization provided by the edge detection.