Table 2

Type I error of the uncorrected and GC or RGC-corrected tests under H0: f0 = f1 = f2 (nominal level is 0.05, a = (500, 1500), b = (1500, 500).
F
 MAF
 K
 Method
 T0
 T1/2
 T1
0.01
 p = 0.2
 200
 Uncorrected
 0.350
 0.557
 0.539
 0.509



GC
 0.032
 0.056
 0.067
 0.045



RGC
 0.063
 0.054
 0.052
 0.055


300
 Uncorrected
 0.335
 0.551
 0.532
 0.497



GC
 0.027
 0.047
 0.057
 0.038



RGC
 0.055
 0.053
 0.051
 0.052

p = 0.45
 200
 Uncorrected
 0.446
 0.543
 0.486
 0.496



GC
 0.085
 0.051
 0.035
 0.053



RGC
 0.052
 0.052
 0.054
 0.049


300
 Uncorrected
 0.464
 0.550
 0.487
 0.512



GC
 0.096
 0.049
 0.037
 0.058



RGC
 0.051
 0.050
 0.052
 0.051
0.02
 p = 0.2
 200
 Uncorrected
 0.473
 0.667
 0.650
 0.633



GC
 0.026
 0.046
 0.061
 0.040



RGC
 0.065
 0.053
 0.052
 0.056


300
 Uncorrected
 0.452
 0.679
 0.662
 0.637



GC
 0.022
 0.048
 0.060
 0.035



RGC
 0.054
 0.050
 0.051
 0.053

p = 0.45
 200
 Uncorrected
 0.591
 0.665
 0.612
 0.627



GC
 0.101
 0.047
 0.038
 0.060



RGC
 0.052
 0.053
 0.054
 0.050


300
 Uncorrected
 0.581
 0.663
 0.610
 0.622



GC
 0.106
 0.047
 0.032
 0.062



RGC
 0.051
 0.052
 0.053
 0.052

The frequencies of null markers are randomly selected from [0.1, 0.5].

Yan et al. BMC Genetics 2009 10:78   doi:10.1186/1471-2156-10-78

Open Data