We grouped the SNPs into four categories: SNPs genotyped on both chips; SNPs genotyped on Affy and imputed for the Illumina controls; SNPs genotyped on Illumina and imputed for the Affy controls; and SNPs imputed for both groups. The false positives found among SNPs genotyped on both platforms can be thought of as a baseline error rate against which to compare the other three groups. For each group of SNPs we summarized the error rates using two quantities: the Genomic Control λ and the percentage of SNPs with p-value less than 5 ×10−8. For χ2 test statistics Xi, i = 1, …, m, the Genomic Control λ is defined as
