Compared to the strategy of adjusting for PCs with large genetic variation, the proposed permutation procedure picks fewer PCs and reduces the over-dispersion factor to a similar or even lower level (Table 5). With either strategy, the over-dispersion factor is slightly decreased from its uncorrected level in the two original studies with internal controls. In the two reconstructed analyses, the over-dispersion level can be reduced substantially and an improved fitting of the Q-Q plot to the diagonal can be achieved. Comparison of Figures 3 with 4 demonstrates the conspicuous effect of PC adjustment in the two reconstructed analyses as this effect is hardly visible on the two original studies with internal controls.
