Table 3.
Proportion of Rejected Null Hypotheses Given the Nominal Type 1 Error in a Real GWAS Dataset when the Phenotype Is Permuted at Random
| Nominal Type I Error | ||||
|---|---|---|---|---|
| 0.05 | 0.01 | 0.001 | 0.0001 | |
| Actual LD | ||||
| PG | 5.27E−2 | 1.11E−2 | 1.01E−3 | 1.27E−4 |
| PG (3 or less SNP) | 5.08E−2 | 1.01E−2 | 1.14E−3 | 8.75E−5 |
| PG (over 3 SNP) | 5.44E−2 | 1.20E−2 | 8.99E−4 | 1.63−4 |
| HapMap CHB LD | ||||
| PG | 5.29E−2 | 1.12E−2 | 1.01E−3 | 1.27E−4 |
| PG (3 or less SNP) | 5.06E−2 | 9.97E−3 | 1.14E−3 | 8.75E−5 |
| PG (over 3 SNP) | 5.51E−2 | 1.23E−2 | 8.99E−4 | 1.63−4 |
The proportions are subject to sampling variation.