A comparative study on gene-set analysis methods for assessing differential expression associated with the survival phenotype

Table 1 The estimated size of the five tests for p = 200 based on 500 iterations

n	m	c _p	GSEA1	GSEA2	GT	WT	GBST
80	20	0.0	0.058	0.052	0.050	0.050	0.050
		0.1	0.060	0.052	0.058	0.058	0.062
		0.3	0.034	0.054	0.054	0.066	0.046
		0.5	0.062	0.042	0.040	0.032	0.052
	50	0.0	0.050	0.048	0.044	0.042	0.052
		0.1	0.050	0.056	0.058	0.058	0.036
		0.3	0.054	0.040	0.054	0.048	0.052
		0.5	0.068	0.060	0.058	0.058	0.060
50	20	0.0	0.054	0.042	0.036	0.032	0.044
		0.1	0.062	0.056	0.046	0.046	0.058
		0.3	0.056	0.036	0.044	0.038	0.052
		0.5	0.046	0.042	0.038	0.046	0.046
	50	0.0	0.070	0.046	0.052	0.044	0.046
		0.1	0.044	0.048	0.042	0.046	0.038
		0.3	0.050	0.038	0.060	0.058	0.060
		0.5	0.046	0.046	0.058	0.040	0.050

Note: n = Sample size; m = the size of gene set; c_p= censoring proportion. GSEA1 = GSEA with the equal weight; GSEA2 = weighted GSEA; GT = Global Test; WT = Wald-type Test; GBST = Global Boost Test

ISSN: 1471-2105