Table 1 Type I errors for four GSA methods: LCT, LCT 2 , SAM-GS and Global-Test
From: Linear combination test for gene set analysis of a continuous phenotype
Type I | 0.005 | 0.01 | 0.05 | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
n | 10 | 10 | 10 | |||||||||
p | 20 | 20 | 20 | |||||||||
p1 = p2 | 5 | 5 | 5 | |||||||||
Method | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 |
LCT | .005 | .003 | .003 | .002 | .012 | .012 | .008 | .009 | .045 | .049 | .044 | .052 |
LCT2 | .006 | .007 | .004 | .003 | .013 | .013 | .009 | .009 | .048 | .057 | .048 | .046 |
SAMGS | .004 | .005 | .006 | .004 | .014 | .012 | .007 | .008 | .044 | .051 | .048 | .050 |
Global | .007 | .008 | .011 | .011 | .013 | .019 | .0117 | .015 | .053 | .052 | .054 | .053 |
n | 20 | 20 | 20 | |||||||||
p | 100 | 100 | 100 | |||||||||
p1 = p2 | 20 | 20 | 20 | |||||||||
Method | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 |
LCT | .010 | .009 | .010 | .010 | .012 | .014 | .014 | .016 | .056 | .053 | .051 | .058 |
LCT2 | .011 | .011 | .009 | .007 | .014 | .017 | .017 | .014 | .056 | .055 | .055 | .054 |
SAMGS | .010 | .011 | .010 | .007 | .012 | .017 | .018 | .014 | .056 | .053 | .052 | .051 |
Global | .004 | .004 | .005 | .006 | .010 | .005 | .006 | .012 | .033 | .041 | .043 | .052 |
n | 50 | 50 | 50 | |||||||||
p | 200 | 200 | 200 | |||||||||
p1 = p2 | 40 | 40 | 40 | |||||||||
Method | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 |
LCT | .010 | .010 | .010 | .011 | .016 | .016 | .015 | .015 | .057 | .055 | .051 | .053 |
LCT2 | .008 | .010 | .011 | .008 | .016 | .016 | .017 | .013 | .053 | .058 | .049 | .059 |
SAMGS | .010 | .008 | .011 | .009 | .015 | .015 | .015 | .019 | .056 | .057 | .051 | .050 |
Global | .004 | .004 | .004 | .001 | .009 | .012 | .012 | .010 | .040 | .059 | .052 | .051 |
n | 100 | 100 | 100 | |||||||||
p | 400 | 400 | 400 | |||||||||
p1 = p2 | 60 | 60 | 60 | |||||||||
Method | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 | ρ = 0.0 | ρ = 0.3 | ρ = 0.6 | ρ = 0.9 |
LCT | .008 | .006 | .003 | .005 | .012 | .010 | .010 | .007 | .049 | .046 | .043 | .034 |
LCT2 | .009 | .006 | .004 | .004 | .012 | .011 | .011 | .010 | .055 | .054 | .042 | .034 |
SAMGS | .006 | .007 | .005 | .008 | .012 | .009 | .010 | .011 | .047 | .050 | .047 | .040 |
Global | .002 | .003 | .003 | .002 | .009 | .005 | .007 | .006 | .056 | .036 | .034 | .034 |