Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset

BMC Bioinformatics

Table 2 Top ten routes for the Platinum Spike dataset.

Rank	Background correction	Probe normalization methods	Probe normalization groups	PM correction	Summarization	Probe set normalization methods	Probe set normalization groups	DEG tests	_rAUC_0.05	TPR_0.05	TP_0.05*
1	gcrma-reb	scaling	all	pmonly	medianpolish	vsn	technical	CyberT	0.848	0.880	1710
2	none	vsn	all	pmonly	medianpolish	constant	all	SAMR	0.847	0.883	1717
3	gcrma-reb	scaling	all	pmonly	medianpolish	vsn	technical	SAMR	0.847	0.877	1705
4	gcrma-reb	constant	all	pmonly	medianpolish	vsn	technical	CyberT	0.846	0.879	1709
5	gcrma-reb	scaling	all	pmonly	medianpolish	vsn	technical	LIMMA	0.846	0.878	1707
6	gcrma-reb	constant	all	pmonly	medianpolish	vsn	technical	LIMMA	0.845	0.878	1706
7	Alchemy								0.845	0.877	1705
8	none	vsn	all	pmonly	medianpolish	constant	all	LIMMA	0.845	0.883	1716
9	none	vsn	all	pmonly	medianpolish	quantiles	technical	Fold Change	0.844	0.877	1704
10	rma	vsn	technical	pmonly	medianpolish	scaling	all	SAMR	0.844	0.878	1707

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