When we attempted to reduce the error inflation using PCs, in Method 1, we observed a complete separation of the two control groups. This complete separation shows the difficulty of controlling for platform effect by simply adjusting for PCs. Including the PCs as covariates in the model is equivalent to including case-control status as a covariate, and thus there does not appear to be a direct way to use those PCs to resolve the error inflation problem. Furthermore, any method using the PCs would likely wash out all differences between cases and controls in a non-null setting. Thus, it makes sense to focus on approaches that filter out problematic SNPs and exclude them from subsequent analysis. Methods 2 and 3 are two such approaches.
