Table 3.

Type I error rates of the different approaches for the small sample scenarios.

Scenario	CAST	PC3CV	LMMCV	LocPerm
50SE-100SE	0.0012	0.0015	0.0012	0.0009
50SE-1000E	0.0016	0.0012	0.0028	0.0008
50SE-1000W	0.0046	0.0011	0.0015	0.0010
50SE-2000W	0.0046	0.0010	0.0016	0.0011
50E-100E	0.0014	0.0015	0.0012	0.0010
50E-1000E	0.0010	0.0010	0.0021	0.0009
50E-1000W	0.0051	0.001	0.0014	0.0010
50E-2000W	0.0050	0.0009	0.0015	0.0011
50World-100W	0.0013	0.0015	0.0012	0.0010
50World-1000E	0.0077	0.0007	0.0053	0.0010
50World-1000W	0.0009	0.0010	0.0021	0.0009
50World-2000W	0.0009	0.0009	0.002	0.0010

The nominal level alpha considered is $\alpha =0.001$. Type I error rates under the lower bound of the 95%PI are displayed in italic and above the upper bound of the 95%PI in bold.

Supplementary Table S3 provides the adjusted 95%PI for the different number of genes tested in each scenario.