1. A method, comprising: a) providing: i) a microarray comprising a first oligonucleotide and second oligonucleotide, said first oligonucleotide comprising a portion of a first allele, said second oligonucleotide comprising a portion of a second allele; ii) a labeled first probe having partial complementarity to a region of said first oligonucleotide; iii) a labeled second probe having complete complementarity to a region of said first oligonucleotide; iv) a labeled third probe having partial complementarity to a region of said second oligonucleotide; and v) a labeled fourth probe having complete complementarity of a region of said second oligonucleotide; b) exposing said first, second, third and fourth probes to said microarray under hybridization conditions to create bound probes; c) determining intensity measurements from said bound probes; and, d) determining a copy number for said first allele and said second allele using said intensity measurements of step c) and an algorithm, said algorithm utilizing an MA ratio.