puma 3.0: improved uncertainty propagation methods for gene and transcript expression analysis

BMC Bioinformatics

Table 5 Area under ROC curves from different methods for U133 GeneChip data

Groups	# of probe-sets			PM-only multi-mgMOS	multi-mgMOS	RMA
	non-DE	DE+	DE-
High	65	21	14	0.9842	0.9952	0.9308
Medium	90	73	82	0.9062	0.8880	0.8827
Low	49	91	171	0.8363	0.8180	0.8147
All	204	185	267	0.8227	0.8130	0.7971

Genes are divided into three groups, labelled as “high”, “medium” and “low”, according to the expression levels. The numbers of “non-DE”, “DE+” and “DE-” probe-sets are shown. AUC is calculated individually for each of the three groups from PM-only multi-mgMOS, multi-mgMOS and RMA combined with PPLR. The overall AUC is also shown in the bottom of the table. The winner is highlighted in bold for each group.

ISSN: 1471-2105