Table 1.
Type I error rates of meta-analysis with two case–control studies for different allele frequencies in the two subpopulations.
| Frequency1 | Study 12 | Study 2 | 10−5 | 10−6 | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Population 1 (2) | Case | Control | Case | Control | PCA | 1 GC | 2 GC | PCA | 1 GC | 2 GC |
| Ran(ran)3 | 1000 | 1000 | 1000 | 1000 | 9.51e–64 | 5.05e–6 | 5.34e–6 | 1.07e–6 | 3.90e–7 | 3.80e–7 |
| 1500 | 1500 | 500 | 500 | 9.88e–6 | 5.00e–6 | 5.29e–6 | 9.19e–7 | 3.90e–7 | 4.60e–7 | |
| 750 | 1500 | 1500 | 750 | 1.04e–5 | 5.08e–6 | 5.50e–6 | 8.50e–7 | 5.20e–7 | 5.70e–7 | |
| 0.4 (0.2) | 1000 | 1000 | 1000 | 1000 | 9.89e–6 | 1.25e–2 | 1.31e–2 | 9.20e–7 | 1.75e–3 | 1.86e–3 |
| 1500 | 1500 | 500 | 500 | 1.01e–5 | 8.04e–3 | 8.49e–3 | 1.01e–6 | 9.77e–4 | 1.05e–3 | |
| 750 | 1500 | 1500 | 750 | 1.02e–5 | 1.26e–2 | 1.30e–2 | 1.03e–6 | 1.76e–3 | 1.85e–3 | |
| 0.6 (0.2) | 1000 | 1000 | 1000 | 1000 | 9.67e–6 | 0.836 | 0.839 | 7.70e–7 | 0.585 | 0.591 |
| 1500 | 1500 | 500 | 500 | 9.43e–6 | 0.763 | 0.769 | 8.60e–7 | 0.478 | 0.486 | |
| 750 | 1500 | 1500 | 750 | 9.86e–6 | 0.837 | 0.841 | 9.30e–7 | 0.588 | 0.594 | |
| 0.8 (0.2) | 1000 | 1000 | 1000 | 1000 | 9.98e–6 | 1.00 | 1.00 | 1.11e–6 | 1.00 | 1.00 |
| 1500 | 1500 | 500 | 500 | 9.61e–6 | 1.00 | 1.00 | 9.50e–7 | 1.00 | 1.00 | |
| 750 | 1500 | 1500 | 750 | 9.69e–6 | 1.00 | 1.00 | 9.20e–7 | 1.00 | 1.00 | |
1
Allele frequencies in the two subpopulations from which cases and controls were sampled for each study.
2
Sample size.
3
Allele frequencies in the two populations of each study were randomly generated.
4
9.51e-6 = 9.51 × 10−6