β-empirical Bayes inference and model diagnosis of microarray data

BMC Bioinformatics

Table 3 The proportion of DE genes ( _{p
1} = 0.05), MR, FPR, FNR with controlled value of FDR at 0.01, and pAUC (at FPR ≤ 0.2) for EB and β -EB approaches averaged over the 50 simulated datasets from the gamma distribution

	p	MR	FPR	FNR	pAUC
In the case of model mis-specification
EB-LNN	0.0309	0.0287	0.0002	0.5776	0.1359
	(0.00054)	(0.0004)	(0.00004)	(0.0081)	(0.0013)
β-EB	0.0371	0.0281	0.0002	0.5704	0.1361
	(0.0006)	(0.00038)	(0.00004)	(0.008)	(0.0014)

The genes with the posterior probabilities of DE ≥ 0.674 for EB-LNN and posterior probabilities of DE ≥ 0.902 for β−EB by controlling FDR at 0.01. The numbers in parentheses are the standard errors for the 50 simulation trails.

ISSN: 1471-2105