BMC Bioinformatics

Table 3 Results of simulation study: Fisher's exact test.

From: Comparative study of gene set enrichment methods

	α= 0.01		α= 0.02		α= 0.03		α= 0.04		α= 0.05
	P-value		P-value		P-value		P-value		P-value
	mean	se	mean	se	mean	se	mean	se	mean	se
1	0.4117	0.0901	0.2789	0.0773	0.1509	0.0411	0.1243	0.0406	0.1137	0.0427
2	0.1961	0.0795	0.0342	0.0171	0.0270	0.0217	0.0287	0.0265	0.0140	0.0120
3	0.0085	0.0033	0.0019	0.0011	0.0024	0.0010	0.0034	0.0020	0.0053	0.0034
4	0.0030	0.0017	0.0016	0.0006	0.0039	0.0018	0.0081	0.0037	0.0113	0.0039
5	2e-04	0.0002	1e-06	0	1e-06	0	6e-07	0	7e-07	0

P-values for the first gene set in the five different scenarios (rows) described in the text. In each column we report the significance level (α) adopted in t-test to find DE genes.

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