1. A method for estimating in a sample the copy number of a genomic region containing at least a first polymorphisms wherein the equation 
 I m =α m,0 +α m,1 ln(δ m +C )+ A m +ε is used to estimate the copy number of an allele of a SNP where m=1,. .. , M is the SNP index, I m is the natural log-transformed probe intensity on SNP m, α m,0 is the SNP-specific optical background, α m,1 is the scaling factor, δ m is the non-specific hybridization, C is the estimated copy number, A m is an affinity term, wherein said affinity term is determined by probe and target fragment sequences, and ε is a random noise term and wherein the parameters of the forumla are estimated using a reference set of samples, where the genotypes of the SNPs in the reference sample are known.