Table 1.

Number of positive genes and estimated FDR

Trait	Method	α = 0.25		α = 0.5		α = 0.75
		No. Pos	FDR	No. Pos	FDR	No. Pos	FDR
Q1	SNP	35.185	0.849	51.625	0.874	65.875	0.884
	GL	31.790	0.791	47.935	0.837	65.100	0.869
	G2	26.785	0.777	39.730	0.823	47.255	0.841
Q2	SNP	3.975	0.281	11.060	0.486	29.905	0.655
	GL	4.175	0.297	12.350	0.503	29.315	0.662
	G2	4.370	0.351	13.755	0.545	27.760	0.684
Q4	SNP	0.325	–	1.215	–	3.210	–
	GL	0.365	–	1.120	–	3.370	–
	G2	0.415	–	1.325	–	2.900	–
D	SNP	3.695	0.324	12.690	0.519	33.940	0.580
	GL	5.225	0.261	17.355	0.374	37.050	0.476
	GS	4.945	0.274	13.615	0.377	34.330	0.437
	G2	5.575	0.284	19.160	0.416	33.880	0.467

SNP, GL, G2, and GS are the SNP-based, gene-based linear, gene-based two-step, and gene-based similarity methods, respectively. α is the predefined value in the BH procedure. “No. POS” is the average number of positives over 200 replicates; and the FDR is the observed false discovery rate.