Table 2.

AUCs for 2-sided test of DE. 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 2-sided tests of DE.

	limma	FC	t-test	Cyber-T	PPLR
mmgMOS	0.903	0.861	0.902	0.919	0.922
MAS5	0.884	0.848	0.879	0.905
CP	0.905	0.873	0.898	0.919	0.889
PLIER	0.898	0.889	0.889	0.911
RMA	0.881	0.885	0.858	0.886	0.860
GCRMA	0.890	0.902	0.883	0.909
DFW	0.764	0.815	0.732	0.703	0.806
MBEI	0.885	0.884	0.870	0.897	0.855
FARMS	0.842	0.891	0.805	0.844	0.772