BMC Bioinformatics

Table 1 Assessment of type I error probabilities

From: Comparative evaluation of gene-set analysis methods

			10 vs. 10 samples			25 vs. 25 samples
	Methods	Type of inference	0	0.5	0.9	0	0.5	0.9
Before standardization	Global Test	The scaled χ²	0.0982	0.0778	0.0722	0.0696	0.0700	0.0686
		Asymptotic	0.0006	0.0128	0.0298	0.0090	0.0328	0.0442
		Permutation	0.0496	0.0434	0.0464	0.0534	0.0554	0.0556
	ANCOVA Global Test	Asymptotic	0.0692	0.1034	0.0898	0.0576	0.0840	0.0736
		Permutation	0.0482	0.0462	0.0458	0.0526	0.0552	0.0562
	SAM-GS	Permutation	0.0498	0.0462	0.0478	0.0514	0.0518	0.0556
After standardization	Global Test	The scaled χ²	0.1090	0.0844	0.0736	0.0734	0.0702	0.0698
		Asymptotic	<0.0001	0.0094	0.0276	0.0036	0.0320	0.0424
		Permutation	0.0524	0.0464	0.0458	0.0524	0.0528	0.0530
	ANCOVA Global Test	Asymptotic	0.0372	0.0848	0.0792	0.0474	0.0838	0.0730
		Permutation	0.0532	0.0462	0.0466	0.0544	0.0542	0.0544
	SAM-GS	Permutation	0.0522	0.0468	0.0470	0.0526	0.0540	0.0542

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ISSN: 1471-2105

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