Table 2.
Derived significance thresholds for the Affymetrix 500K data.
| Chromo- some |
Number of SNPs |
Permutation | simpleM | Keff | Bonferroni | |||
|---|---|---|---|---|---|---|---|---|
| Meff | αp | Meff | αp | w=20 | αp | αp | ||
| 1 | 30655 | 17011 | 3.02E-06 | 18079 | 2.84E-06 | 20980 | 2.44E-06 | 1.63E-06 |
| 2 | 32107 | 18474 | 2.78E-06 | 19193 | 2.67E-06 | 22041 | 2.33E-06 | 1.56E-06 |
| 3 | 26573 | 15279 | 3.36E-06 | 15704 | 3.27E-06 | 18054 | 2.84E-06 | 1.88E-06 |
| 4 | 24773 | 13534 | 3.79E-06 | 14363 | 3.57E-06 | 16603 | 3.09E-06 | 2.02E-06 |
| 5 | 25414 | 12829 | 4.00E-06 | 14941 | 3.43E-06 | 17209 | 2.98E-06 | 1.97E-06 |
| 6 | 25552 | 14610 | 3.51E-06 | 14638 | 3.50E-06 | 17077 | 3.00E-06 | 1.96E-06 |
| 7 | 20655 | 12108 | 4.24E-06 | 12470 | 4.11E-06 | 14243 | 3.60E-06 | 2.42E-06 |
| 8 | 21494 | 12268 | 4.18E-06 | 12749 | 4.02E-06 | 14617 | 3.51E-06 | 2.33E-06 |
| 9 | 18140 | 9519 | 5.39E-06 | 11194 | 4.58E-06 | 12737 | 4.03E-06 | 2.76E-06 |
| 10 | 22293 | 12681 | 4.04E-06 | 13017 | 3.94E-06 | 14980 | 3.42E-06 | 2.24E-06 |
| 11 | 20621 | 10719 | 4.79E-06 | 11931 | 4.30E-06 | 13654 | 3.76E-06 | 2.42E-06 |
| 12 | 19487 | 10214 | 5.02E-06 | 11626 | 4.41E-06 | 13326 | 3.85E-06 | 2.57E-06 |
| 13 | 14859 | 8070 | 6.36E-06 | 8766 | 5.85E-06 | 10073 | 5.09E-06 | 3.36E-06 |
| 14 | 12151 | 6592 | 7.78E-06 | 7438 | 6.90E-06 | 8439 | 6.08E-06 | 4.11E-06 |
| 15 | 10997 | 6832 | 7.51E-06 | 7112 | 7.21E-06 | 7945 | 6.46E-06 | 4.55E-06 |
| 16 | 11808 | 7067 | 7.26E-06 | 7692 | 6.67E-06 | 8539 | 6.01E-06 | 4.23E-06 |
| 17 | 8900 | 5371 | 9.55E-06 | 5743 | 8.93E-06 | 6372 | 8.05E-06 | 5.62E-06 |
| 18 | 11421 | 7134 | 7.19E-06 | 6981 | 7.35E-06 | 7890 | 6.50E-06 | 4.38E-06 |
| 19 | 5062 | 3052 | 1.68E-05 | 3437 | 1.49E-05 | 3762 | 1.36E-05 | 9.88E-06 |
| 20 | 9739 | 5851 | 8.77E-06 | 6024 | 8.51E-06 | 6744 | 7.61E-06 | 5.13E-06 |
| 21 | 5668 | 3084 | 1.66E-05 | 3439 | 1.49E-05 | 3854 | 1.33E-05 | 8.82E-06 |
| 22 | 4844 | 3042 | 1.69E-05 | 3223 | 1.59E-05 | 3575 | 1.43E-05 | 1.03E-05 |
| genome- wide |
383213 | 208408 | 2.46E-07 | 229760 | 2.23E-07 | 262714 | 1.95E-07 | 1.30E-07 |
The permutation thresholds were calculated using 10,000 random shuffles.
The experiment-wise error rates for each chromosome and the genome-wide adjustment was set at αe = 0.05.
αp: point-wise error rate.
Meff: the effective number of independent tests.
w=20: window size is set equal to 20.