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Performance comparisons among three PC selection strategies in simulations where replicated datasets are assembled from the two GWAS in the CGEMS. Results are summarized based on 100 generated datasets, with each consisting of 800 cases and 800 controls. (A) Boxplots of number of chosen PCs; (B) Boxplots of empirical type I errors under the significance level of 0.05 and (C) Boxplots of over-dispersion factors.
