Results from the different array sets were analyzed separately to allow for the possibility of different levels of pooling error in each experiment. The results for each SNP were then combined by calculating a composite version of T_2_X, which weighted the result by the inverse of the estimated variance for that SNP – the estimated variance comprised the binomial sampling variance, together with the terms 2vare_pool_2 and varSNPspecific. In cases where a particular SNP passed quality control for a subset of pools, only the relevant pools contributed to the test statistic. That is, failing quality control for some pools did not necessarily remove that SNP completely from the analysis (although the sample size for that SNP would be reduced)
