Table 3.

AUCs for 1-sided test of up-regulation. This table shows AUC values for different combinations of summarization and DE detection methods. The 10 highest AUC values are highlighted in bold. Note that the PPLR method is only applicable to summarization methods that give uncertainty estimates as well as mean expression levels for each probeset. These results were calculated using only the equal spike-ins as true negatives, and all spike-ins with FC > 1 as true positives. A post-summarization loess normalization using the equal-valued spike-ins was used. The results in this table are for 1-sided tests of up-regulation.

	limma	FC	t-test	Cyber-T	PPLR
mmgMOS	0.940	0.920	0.938	0.949	0.951
MAS5	0.924	0.908	0.921	0.934
CP	0.940	0.928	0.935	0.948	0.932
PLIER	0.934	0.929	0.930	0.941
RMA	0.929	0.932	0.914	0.932	0.917
GCRMA	0.926	0.946	0.921	0.944
DFW	0.817	0.918	0.794	0.830	0.912
MBEI	0.928	0.928	0.920	0.934	0.915
FARMS	0.883	0.938	0.847	0.908	0.893