Evaluating methods for ranking differentially expressed genes applied to microArray quality control data

Kadota, Koji; Shimizu, Kentaro

doi:10.1186/1471-2105-12-227

BMC Bioinformatics

Table 2 Average AUC values for ABI, AG1, GEH, and ILM data

From: Evaluating methods for ranking differentially expressed genes applied to microArray quality control data

Technology	TAQ	TAQ	TAQ	TAQ	GEX	GEX	GEX	GEX
Comparison	AB	AB	CD	CD	AB	AB	CD	CD
Metric	FDR	AD	FDR	AD	FDR	AD	FDR	AD
#DEGs	817	553	767	351	144	106	114	60
ABI
WAD	66.18	74.77	67.30	77.46	70.71	74.49	70.01	76.62
AD	63.45	75.49	62.88	78.92	65.33	71.14	61.86	71.10
FC	62.93	75.00	62.27	78.63	64.95	70.76	60.84	70.42
RP	62.46	75.45	60.28	79.58	64.17	70.43	58.37	68.82
modT	66.03	73.63	67.62	76.75	71.27	74.84	70.54	77.31
samT	64.00	75.63	63.80	79.23	66.36	71.92	63.34	72.57
shrT	65.60	74.91	66.86	78.05	69.75	74.12	68.80	76.54
ibmT	66.37	73.43	67.93	76.41	71.99	75.26	71.12	77.39
AG1
WAD	66.73	73.14	67.39	74.69	71.28	75.58	72.67	77.80
AD	64.60	75.20	64.41	78.48	65.73	73.53	65.75	75.65
FC	64.32	75.15	63.01	77.55	65.42	73.58	63.98	73.95
RP	64.37	75.20	65.03	79.35	65.38	72.78	66.45	76.02
modT	65.66	74.25	66.00	76.42	68.80	74.78	70.44	77.75
samT	64.26	74.29	64.77	78.66	66.34	73.79	66.49	76.24
shrT	65.47	74.78	65.67	77.76	68.01	74.65	69.19	77.89
ibmT	65.97	74.32	66.34	76.59	69.80	75.61	71.22	78.86
GEH
WAD	74.03	78.39	74.64	79.38	76.18	79.19	76.87	81.26
AD	71.27	78.60	71.24	80.36	70.50	75.64	70.09	77.28
FC	71.16	78.50	70.81	80.21	70.30	75.48	69.84	77.05
RP	71.19	78.68	70.97	80.62	70.58	75.71	69.93	77.54
modT	71.90	78.04	71.74	79.01	71.18	75.46	72.25	78.26
samT	71.40	78.66	71.54	80.48	70.61	75.69	70.72	77.76
shrT	72.02	78.64	72.12	80.13	71.30	75.89	72.19	78.63
ibmT	71.87	78.01	71.70	78.99	71.14	75.41	72.27	78.31
ILM
WAD	79.13	82.49	78.94	82.63	83.25	84.79	82.09	83.88
AD	77.43	83.85	76.33	84.64	79.92	83.71	77.93	82.93
FC	77.39	83.83	76.35	84.63	79.90	83.77	78.14	83.17
RP	77.58	84.23	76.10	85.28	79.81	83.94	77.97	84.13
modT	77.45	82.98	76.73	83.56	80.64	83.78	78.70	82.96
samT	77.42	83.63	76.53	84.39	80.08	83.70	78.28	83.02
shrT	77.39	83.05	76.72	83.58	80.49	83.73	78.64	82.93
ibmT	77.94	82.96	77.53	83.48	81.37	84.04	79.77	83.31

Average AUC values across three test sites. Reminder of legend is the same as in Table 1.

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