A package based on a normalization method that estimates both biological and nonrelevant effects in an alternate, iterative manner, accurately eliminating irrelevant effects. ITALICS uses a normalization algorithm for Affymetrix SNP arrays. This method was designed for the normalization and analysis of DNA copy number and significantly outperformed other methods, such as CNAT 3.0, CNAT 4.0, CNAG and GIM, in terms of SNR and can also be used to correct for experimental artifacts due to spatial effects. This method was validated by QPCR and accurately detected the breakpoints in genomic profiles. It could therefore be used to improve the characterization of samples in genomic studies.