Table 4.
False positive error rate under the null hypothesis, and true discovery rate (false positive error rate) under alternative hypotheses 1 when the Clayton's stepwise approach is used to select a subset of SNPs.
| Odds | Sample Sizes | ||||
| Ratios | 250 × 2 | 500 × 2 | 1,000 × 2 | ||
| Null Hypothesis | |||||
| 5.5 | 5.2 | 5.0 | |||
| Alternative Hypothesis with a Single Functional SNP: 0(ref) and 1 | |||||
| 1.5 | 65.7/70.0/5.5 | 71.3/87.0/5.1 | 74.3/100/5.0 | ||
| 2.0 | 71.3/100/5.3 | 71.1/100/5.0 | 85.0/100/5.0 | ||
| 3.0 | 80.7/100/5.0 | 89.3/100/5.0 | 94.0/100/5.0 | ||
| Alternative Hypothesis with Two SNPs: 00 (ref), 01, 10 & 11 | |||||
| Scenario 1 | |||||
| 1.0 | 1.3 | 1.0 | 14.3/51.0/6.1 | 31.3/68.8/5.7 | 32.1/77.0/6.3 |
| 1.0 | 1.5 | 1.0 | 29.2/61.0/7.0 | 42.2/72.1/7.1 | 33.2/78.2/7.2 |
| 1.0 | 2.0 | 1.0 | 36.5/92.2/6.0 | 51.7/95.0/5.3 | 71.2/100/4.4 |
| 1.0 | 3.0 | 1.0 | 51.1/98.2/5.0 | 60.3/98.8/4.1 | 82.4/99.8/4.0 |
| 1.0 | 5.0 | 1.0 | 52.0/99.1/4.3 | 61.2/100/4.0 | 100/100/4.0 |
| Scenario 2 | |||||
| 1.0 | 1.0 | 1.3 | 7.9/45.2/5.5 | 21.4/65.0/5.4 | 19.7/71.2/6.3 |
| 1.0 | 1.0 | 1.5 | 7.8/51.4/5.3 | 14.5/55.1/5.2 | 21.7/80.1/6.3 |
| 1.0 | 1.0 | 2.0 | 7.2/55.2/6.1 | 19.9/74.5/6.0 | 30.0/82.1/6.0 |
| 1.0 | 1.0 | 3.0 | 17.8/93.0/6.0 | 23.4/94.4/5.4 | 25.4/95.7.0/5.4 |
| 1.0 | 1.0 | 5.0 | 23.4/90.8/5.7 | 32.9/88.1/6.2 | 34.3/89.2/5.4 |