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Table 5 Power of MDR with and without omnibus permutation testing and false positive rate with permutation testing.

From: The effect of alternative permutation testing strategies on the performance of multifactor dimensionality reduction

Epistasis Model

   

Number of Functional Loci

Minor Allele Frequency

Heritability

Power (%) Without Permutation Testing

Power (%) With Permutation Testing

False Positive Rate (%) With Permutation Testing

2

0.2

3%

   

2

0.2

2%

90

88

0

2

0.2

1.5%

94

91

1

2

0.2

1%

70

56

6

2

0.2

0.5%

18

14

4

2

0.4

3%

93

93

2

2

0.4

2%

93

92

5

2

0.4

1.5%

95

91

1

2

0.4

1%

85

71

6

2

0.4

0.5%

25

11

0

3

0.2

3%

69

69

2

3

0.2

2%

85

85

2

3

0.2

1.5%

20

18

5

3

0.2

1%

6

2

6

3

0.2

0.5%

6

2

4

3

0.4

3%

89

89

1

3

0.4

2%

55

54

3

3

0.4

1.5%

40

34

2

3

0.4

1%

6

4

2

3

0.4

0.5%

3

0

1

4

0.2

3%

68

68

4

4

0.2

2%

59

57

8

4

0.2

1.5%

11

10

4

4

0.2

1%

10

9

2

4

0.2

0.5%

1

0

1

4

0.4

3%

60

52

1

4

0.4

2%

36

25

5

4

0.4

1.5%

4

4

7

4

0.4

1%

3

2

6

4

0.4

0.5%

0

0

3

5

0.2

3%

35

35

3

5

0.2

2%

3

3

3

5

0.2

1.5%

1

0

2

5

0.2

1%

20

11

4

5

0.2

0.5%

0

0

1

5

0.4

3%

15

10

0

5

0.4

2%

3

2

6

5

0.4

1.5%

0

0

9

5

0.4

1%

0

0

0

5

0.4

0.5%

0

0

5