Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity

Table 2 Average AUC values for Datasets 3–26 and 27–38

Method	PLIER	VSN	FARMS	mmgMOS	MBEI	GCRMA	MAS	RMA	DFW	Average
Datasets 3–26
WAD	89.15	90.97	91.58	94.84	88.19	92.67	96.74	91.37	91.41	91.88
AD	87.32	92.96	92.47	93.13	89.14	93.42	93.76	93.10	92.24	91.95
FC	86.20	92.92	92.49	92.82	89.71	93.16	93.63	93.12	92.24	91.81
RP	92.01	92.48	93.06	92.20	90.07	93.23	91.51	92.54	92.53	92.18
modT	85.43	90.70	89.23	91.91	86.79	91.19	95.67	91.38	90.11	90.27
samT	85.25	90.94	89.40	92.99	87.09	91.07	95.95	91.23	89.96	90.43
shrinkT	84.65	90.62	-	92.56	86.89	92.12	95.73	91.32	91.45	90.67
ibmT	86.27	91.02	90.04	93.11	87.10	91.06	96.34	91.77	90.25	90.78
Datasets 27–38
WAD	91.30	95.41	93.55	92.36	93.39	95.75	92.42	96.73	94.09	93.89
AD	89.01	96.22	93.81	86.99	93.11	96.18	87.41	96.77	94.22	92.64
FC	88.82	96.20	93.81	85.92	92.94	96.06	88.23	96.73	94.22	92.55
RP	91.57	96.53	94.76	86.94	93.53	96.25	84.55	96.53	94.67	92.81
modT	89.28	94.53	91.62	89.61	90.50	93.33	90.90	95.28	92.36	91.93
samT	88.53	95.08	91.90	89.14	90.49	93.60	90.31	95.70	92.05	91.87
shrinkT	88.56	94.04	-	89.85	90.13	94.48	90.97	94.85	93.68	92.07
ibmT	89.89	94.80	89.95	90.60	90.66	93.67	91.92	95.49	92.43	92.16
Average	88.33	93.46	91.98	90.94	89.98	93.58	92.25	93.99	92.37

As statistics for shrinkT frequently include infinities, AUC values for FARMS/shrinkT could not be calculated. Note that AUC values for each dataset are given in the additional file [see Additional file 1].

ISSN: 1748-7188