Table 1.

Simulation study results comparing SPCA, PCA, GSEA, GSEAlm, and Fisher's Exact Test

Scene	N_Genes	r_mean	r_variance	Area Under Curve						Av.p-value for Gene Set 1
				SPCA	PCA	GSEA	GSEAlm	Fisher (0.05)	Fisher (0.1)	SPCA	PCA	GSEA	GSEAlm	Fisher (0.05)	Fisher (0.1)
1	5	0.1	0.5	0.898	0.758	0.740	0.567	0.674	0.699	0.059	0.410	0.259	0.428	0.656	0.606
2	5	0.1	1	0.956	0.716	0.780	0.566	0.825	0.849	0.028	0.271	0.219	0.427	0.358	0.308
3	5	0.1	1.5	0.973	0.850	0.799	0.557	0.900	0.899	0.018	0.146	0.203	0.436	0.205	0.206
4	5	0.2	0.5	0.895	0.572	0.727	0.614	0.749	0.774	0.060	0.417	0.275	0.380	0.508	0.459
5	5	0.2	1	0.947	0.740	0.781	0.604	0.875	0.874	0.032	0.250	0.219	0.389	0.260	0.259
6	5	0.2	1.5	0.963	0.848	0.758	0.604	0.890	0.899	0.022	0.147	0.219	0.387	0.205	0.206
7	10	0.1	0.5	0.962	0.707	0.788	0.613	0.775	0.774	0.025	0.283	0.211	0.383	0.458	0.458
8	10	0.1	1	0.993	0.902	0.840	0.612	0.925	0.924	0.006	0.092	0.158	0.384	0.157	0.154
9	10	0.1	1.5	0.999	0.980	0.908	0.600	0.975	0.975	0.001	0.019	0.087	0.394	0.054	0.053
10	10	0.2	0.5	0.965	0.714	0.857	0.710	0.850	0.874	0.023	0.277	0.140	0.282	0.311	0.262
11	10	0.2	1	0.995	0.887	0.868	0.700	0.925	0.924	0.006	0.110	0.129	0.294	0.156	0.153
12	10	0.2	1.5	0.999	0.995	0.887	0.678	0.975	0.999	0.001	0.005	0.113	0.316	0.053	0.004

Fisher(0.05) = Fisher's exact test using 0.05 FDR level as significance level cutoff; Fisher(0.1)=Fisher's exact test using 0.1 FDR level as significance level cutoff; r_mean=mean of association measure r; r_variance=variance of association measure r; see text for details of simulation experiments.