We investigated whether we could capture the platform effect using PCs. To do this, we used EIGENSTRAT (http://genepath.med.harvard.edu/~reich/Software.htm) (Patterson et al. 2006; Price et al. 2006). In a typical application of this program, the first few PCs are calculated and included as covariates in logistic regression to capture and control for population stratification. An example in Price et al. (2006) suggests the possibility of some components capturing lab and batch effects as well. We calculated the first ten PCs and assessed how well they correlated with platform effect. Then we attempted to include these components as covariates in logistic regression models predicting case-control status from each SNP. We did this in two ways: first, we calculated the PCs using all measured and imputed SNPs; second, we restricted to SNPs in each of the four categories, and calculated PCs using only those SNPs (e.g., using only SNPs measured on one chip and imputed in the other).
