We then evaluated the effectiveness of IQS in the situation where cases and controls are genotyped on different platforms. We randomly divided the SAGE data into two subgroups labeled “cases” and “controls”. In “cases”, original genotypes were retained for SNPs on the Illumina 550 K array; and then imputation was performed to obtain the full Illumina 1 M array. In “controls”, original genotypes were retained for all SNPs on the Illumina 1 M array. This process is equivalent to combining cases genotyped by the Illumina 550 K array and controls genotyped by the Illumina 1 M array.
