Table 2.

The number of significant gene sets on the four data sets at FDR 1% with linear combination strategy.

Dataset	GS	DS	0.1	0.2	0.3	0.4	0.5	0.6	0.7	0.8	0.9	DE
Artificial	c2	1550	982	1389	1656	1773	1757	1569	1247	696	261	64
	c5	647	326	479	681	766	747	675	558	354	158	66
Cancer	c2	4	3	4	10	14	16	16	16	14	12	12
	c5	11	11	20	14	13	9	6	2	2	1	1
BA46	c2	0	1	1	2	3	3	2	4	3	2	2
	c5	0	2	2	2	2	2	2	2	2	1	0
BA22	c2	0	0	0	0	0	0	0	0	0	0	0
	c5	0	0	0	0	1	1	1	1	0	0	0

For the full results, see Supplementary Tables S1-S4.

GS: gene set category; DS: DS-only GSEA; DE: DE-only GSEA; 0.1,...,0.9: weights α.