Table 2. Four gene sets that satisfied p < 0.001 in both the Affymetrix and Illumina datasets and their p-values, FDR, accuracy and AUC.

P-values and FDR were calculated using the “gage” R package, and the accuracy was obtained from leave-one-out cross validation. AUC generated by K-OPLS for scoring classifiers of four gene sets.

Gene Sets	Affymetrix				Illumina
	p-value	FDR	accuracy (%)	AUC	p-value	FDR	accuracy (%)
DNA replication	9.81E-05	0.008	87	0.939	6.62E-12	1.17E-09	100
Valine, leucine and isoleucine degradation	0.000729	0.016	73	0.816	0.000251	0.007	100
Cytokine-cytokine receptor interaction	0.000852	0.041	87	0.841	0.000575	0.010	100
Systemic lupus erythematosus	0.000978	0.041	93	0.982	0.000553	0.010	100