We performed a PCA on the joint sample including subjects from both studies. A representation of each subject by its first 2 PCs in a scatter plot stratified by the study (PLCO or NHS) is shown (Figure 2). Visual inspection of Figure 2A and 2B indicates that patterns of population structure of the two studies are indeed similar in the plane of the first 2 PCs. However, further scrutiny reveals very significant difference between the two studies. Between-studies comparisons using the Wilcoxon rank-sum test suggest that the subjects from the two studies have significantly different distributions (with P-values <10−4) along each of the top 4 PC directions.
