Table 3.
Method | Size | Control-Only | Control + Affected (LOW)a | Control + Affected (MOD)a |
---|---|---|---|---|
min-adj p | 10−2 | 1.32 × 10−2 | 1.32 × 10−2 | 1.31 × 10−2 |
10−3 | 1.70 × 10−3 | 1.71 × 10−3 | 1.68 × 10−3 | |
10−4 | 2.58 × 10−4 | 2.61 × 10−4 | 2.47 × 10−4 | |
10−5 | 4.15 × 10−5 | 4.14 × 10−5 | 3.77 × 10−5 | |
(weighted) traditional GEE | 10−2 | 1.62 × 10−2 | 1.63 × 10−2 | 1.60 × 10−2 |
(4-DF; I/E/U) | 10−3 | 2.59 × 10−3 | 2.61 × 10−3 | 2.51 × 10−3 |
10−4 | 5.32 × 10−4 | 5.37 × 10−4 | 4.89 × 10−4 | |
10−5 | 1.09 × 10−4 | 1.10 × 10−4 | 9.29 × 10−5 | |
(weighted) SMAT | 10−2 | 1.17 × 10−2 | 1.17 × 10−2 | 1.16 × 10−2 |
(1-DF; I/E) | 10−3 | 1.41 × 10−3 | 1.41 × 10−3 | 1.42 × 10−3 |
10−4 | 1.89 × 10−4 | 1.90 × 10−4 | 1.94 × 10−4 | |
10−5 | 2.89 × 10−5 | 2.89 × 10−5 | 2.71 × 10−5 | |
(weighted) SMAT | 10−2 | 1.19 × 10−2 | 1.19 × 10−2 | 1.16 × 10−2 |
(1-DF; U) | 10−3 | 1.44 × 10−3 | 1.42 × 10−3 | 1.41 × 10−3 |
10−4 | 1.86 × 10−4 | 1.86 × 10−4 | 1.83 × 10−4 | |
10−5 | 3.09 × 10−5 | 3.10 × 10−5 | 2.81 × 10−5 |
Empirical size results for simulated data sets and assuming the true correlation among the phenotypes is unstructured, as given in Table 1. For multiple phenotype analyses, independent (I), exchangeable (E), and unstructured (U) working correlation structures were considered. The results from the 4-DF GEE test with I, E, and U working correlation structures are nearly identical. The results from the 1-DF SMAT with the I and E working correlation structures are nearly identical.
LOW and MOD refer to disease prevalence and respectively.