Using 0.05 as the P-value threshold for selecting PCs with large variation, four or five PCs were chosen for the four studies under investigation (Table 1). Moreover, results from Table 5 suggest that adjustment of a PC with significantly large variation may not necessarily reduce the over-dispersion factor if cases and controls have comparable distribution over that PC. For example, in the original prostate cancer scan, the cases and controls have very similar genetic background as seen in the 2nd PC direction (see Table 5). In this case, compared to adjustment of the first PC, adding the 2nd PC into the adjustment does not reduce the over-dispersion factor.
