Array-based Comparative Genomic Hybridization (aCGH) is a powerful tool to study copy number alterations (CNA) in human diseases such as cancers. This high-throughput technique allows simultaneous measuring of copy number for thousands of genes throughout the genome. Copy number alterations are measured using log2 ratios of the fluorescence intensities from two channels (Cy3 and Cy5), one for the target sample and the other for the reference sample. For a given gene (or region), a negative log2 ratio is an indication of a loss, and a positive log2 ratio is an indication of a gain. If the log2 ratio equals zero, the target sample and the reference sample have the same copy number for that given gene (or region).