... standard benchmarks for Affymetrix SNP chip analysis is analogous to that already done for the sister technology of Affymetrix expression arrays, the so-called Affycomp [29] Materials and methods ... between the center of region AA and AB and the center of AB and BB Finally, we noted that accuracy is slightly different for homozygous and heterozygous genotypes Heterozygous genotypes appear to ... a genotype call and calculate a confidence measure for any given pair (sense and antisense) of observed log-ratios: Mi,j,+ and Mi,j,- Notice that these M values can come from any study, and we...