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Table 3 False positive rates for n-locus permutation distributions.

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

Epistasis Model N-Locus Permutation Distribution False Positive Rate (%)
Number of Functional Loci Minor Allele Frequency Heritability 1 Locus 2 Locus 3 Locus 4 Locus 5 Locus
2 0.2 3% 4 0 100 100 100
2 0.2 2% 2 0 84 76 62
2 0.2 1.5% 3 0 89 78 57
2 0.2 1% 3 1 50 55 33
2 0.2 0.5% 3 1 17 5 6
2 0.4 3% 4 0 95 89 76
2 0.4 2% 7 0 96 93 69
2 0.4 1.5% 7 0 82 57 45
2 0.4 1% 4 1 31 24 19
2 0.4 0.5% 6 3 6 13 8
3 0.2 3% 3 5 0 100 100
3 0.2 2% 2 36 0 100 94
3 0.2 1.5% 2 65 33 67 48
3 0.2 1% 4 40 22 22 22
3 0.2 0.5% 2 1 1 3 3
3 0.4 3% 6 10 0 100 93
3 0.4 2% 5 46 2 57 46
3 0.4 1.5% 3 43 4 61 26
3 0.4 1% 11 12 13 17 4
3 0.4 0.5% 5 10 5 14 6
4 0.2 3% 9 46 85 0 95
4 0.2 2% 4 31 64 4 90
4 0.2 1.5% 1 18 26 11 20
4 0.2 1% 6 5 6 8 18
4 0.2 0.5% 6 9 8 23 11
4 0.4 3% 6 16 63 7 77
4 0.4 2% 0 7 24 3 23
4 0.4 1.5% 4 5 15 3 5
4 0.4 1% 1 14 7 4 12
4 0.4 0.5% 2 11 9 9 3
5 0.2 3% 4 21 51 64 21
5 0.2 2% 1 10 27 64 23
5 0.2 1.5% 1 1 6 6 9
5 0.2 1% 7 14 20 18 13
5 0.2 0.5% 3 2 3 3 5
5 0.4 3% 7 5 11 16 6
5 0.4 2% 1 6 6 12 7
5 0.4 1.5% 7 3 7 8 5
5 0.4 1% 0 2 10 10 6
5 0.4 0.5% 10 6 3 4 6