The distribution of the 180 discrepancies is also nonrandom. There are no occurrences of one platform calling a genotype a homozygote and the other platform calling the genotype the opposite homozygote. Rather, all of the discrepancies result from a genotype being called homozygous by one platform and heterozygous by the other. In 86% of the discrepancies, Illumina calls the genotype heterozygous and Affymetrix calls it homozygous.
