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	rAUC0.05	TPR0.05	TP0.05*
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

*the number of correctly detected DEGs at false positive rate cutoff 0.05.