1. A method for calling genotypes from a probe array experiment, comprising: contacting a genotyping probe array with a DNA sample to obtain a hybridized sample; obtaining hybridization intensity information from the hybridized sample; normalizing probe intensity data; transforming the data by clustering the data for each genetic loci of interest to obtain transformed data; dividing the transformed data into trial genotypes by generating genotyping calls; calculating the highest log-likelihood of data; and assigning a genotype to the data.