Table 3. The median (Q1 – Q3)* numbers of SNPs selected in the first stage of a two-stage GWA study using the FNR-based approach for the five simulation models, given pre-specified multi-testing powers (50%, 60%, 70%, 80%and 90%) and different parameter λ values (10-5, 5×10-5, 10-4, and 10-3), based on 100 replicates.
| Model (#of causal SNPs) | Parameter values | Pre-specified multi-testing powers | ||||
|---|---|---|---|---|---|---|
|
| ||||||
| 50% | 60% | 70% | 80% | 90% | ||
| Model 1 (5) | λ = 10−5 | 3(2-5) | 4(2-6) | 5(3-7) | 6(4-9) | 8(4-11) |
| λ =5 × 10−5 | 5(1-10) | 7(1-14) | 9(2-19) | 12(2-25) | 15(2-30) | |
| λ = 10−4 | 10(2-20) | 16(3-30) | 21(3-39) | 28(4-46) | 36(4-54) | |
| λ = 10−3 | 130(1-254) | 180(1-314) | 223(1-379) | 284(1-418) | 335(1-464) | |
| Model 2 (10) | λ = 10−5 | 7(4-8) | 8(5-11) | 10(7-13) | 12(8-16) | 14(9-18) |
| λ = 5 × 10−5 | 11(8-17) | 16(11-22) | 22(15-28) | 27(18-36) | 35(21-43) | |
| λ = 10−4 | 19(11-26) | 25(15-35) | 34(19-43) | 46(26-55) | 56(38-66) | |
| λ = 10−3 | 172(85-246) | 246(138-317) | 314(187-378) | 395(228-465) | 476(273-525) | |
| Model 3 (15) | λ = 10−5 | 12(10−15) | 15(13-19) | 18(15-22) | 21(18-26) | 25(21-30) |
| λ = 5×10−5 | 24(18-29) | 31(24-37) | 39(31-45) | 46(38-55) | 56(46-64) | |
| λ = 10−4 | 35(27-41) | 45(36-53) | 58(47-68) | 70(61-83) | 86(74-100) | |
| λ = 10−3 | 194(147-229) | 272(204-314) | 349(280-412) | 430(372-491) | 535(461-581) | |
| Model 4 (20) | λ = 10−5 | 19(16-23) | 24(20-28) | 28(24-33) | 33(28-39) | 38(33-44) |
| λ = 5 × 10−5 | 34(30-39) | 43(36-50) | 52(45-60) | 63(54-71) | 73(64-84) | |
| λ = 10−4 | 48(38-54) | 62(50-68) | 75(63-86) | 92(78-103) | 111(95-124) | |
| λ = 10−3 | 193(159-228) | 272(215-312) | 355(304-419) | 456(392-523) | 573(506-628) | |
| Model 5 (25) | λ = 10−5 | 15(11-17) | 18(14-22) | 21(17-25) | 25(20-29) | 29(23-34) |
| λ = 5 × 10−5 | 28(22-32) | 36(29-40) | 44(37-49) | 54(44-60) | 63(54-71) | |
| λ = 10−4 | 40(32-47) | 52(44-61) | 65(54-76) | 81(65-91) | 94(83-108) | |
| λ = 10−3 | 212(170-257) | 288(228-339) | 379(311-428) | 461(399-528) | 566(508-627) | |
*
Q1: 1st quartile Q3: 3rd quartile
λ: parameter used for estimating number of null hypotheses.