report advocating the use of public controls (Zhuang et al., 2010). Batch genotype effects, before and after accounting for systematic batch effects across all SNPs, had either a negative or positive impact on power (Tables 4 and 5) and resulted in increased type I error rates for the SNP under consideration (Supplementary Table 8). Still, the impact of batch genotype effects on the overall family-wise error rate was small after applying the Genomic Control method (Reich and Goldstein, 2001) to account for the systematic inflation.
