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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.

From: A systematic search for SNPs/haplotypes associated with disease phenotypes using a haplotype-based stepwise procedure

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