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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