An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

Su, Zhenqiang; Fang, Hong; Hong, Huixiao; Shi, Leming; Zhang, Wenqian; Zhang, Wenwei; Zhang, Yanyan; Dong, Zirui; Lancashire, Lee J; Bessarabova, Marina; Yang, Xi; Ning, Baitang; Gong, Binsheng; Meehan, Joe; Xu, Joshua; Ge, Weigong; Perkins, Roger; Fischer, Matthias; Tong, Weida

doi:10.1186/s13059-014-0523-y

Table 6 The performance of k-NN models in predicting microarray and RNA-Seq validation samples based on the SEQC NB data

From: An investigation of biomarkers derived from legacy microarray data for their utility in the RNA-seq era

Direction	End point	Gene set	Predicto mg microarray validation data				Predicting RNA-Seq validation data				T-index
			Accuracy		AUC		Accuracy		AUC
			Mean	95% CI	Mean	95% CI	Mean	95% CI	Mean	95% CI
Models developed from microarray	A*	A	0.728	0.659-0.775	0.698	0.633-0.752	0.706	0.606-0.763	0.678	0.596-0.747	0.712
	A*	B	0.730	0.655-0.775	0.694	0.619-0.749	0.709	0.640-0.755	0.671	0.610-0.730	0.714
	B*	A	0.786	0.751-0.815	0.662	0.600-0.719	0.792	0.743-0.831	0.621	0.547-0.738	0.791
	B*	B	0.785	0.743-0.821	0.638	0.572-0.708	0.764	0.663-0.815	0.621	0.521-0.737	0.768
	C*	A	0.988	0.983-0.992	0.988	0.983-0.992	0.990	0.975-0.992	0.990	0.977-0.992	0.990
	C*	B	0.982	0.971-0.992	0.983	0.974-0.992	0.984	0.975-0.992	0.985	0.976-0.995	0.984
	D*	A	0.928	0.860-0.971	0.907	0.831-0.962	0.890	0.790-0.949	0.860	0.728-0.937	0.891
	D*	B	0.918	0.816-0.982	0.900	0.781-0.978	0.868	0.746-0.956	0.841	0.736-0.945	0.870
	E*	A	0.625	0.522-0.711	0.540	0.446-0.637	0.627	0.456-0.733	0.529	0.440-0.636	0.626
	E*	B	0.564	0.456-0.661	0.489	0.394-0.573	0.516	0.278-0.711	0.497	0.429-0.575	0.533
	F*	A	0.516	0.433-0.600	0.515	0.432-0.597	0.532	0.433-0.622	0.521	0.438-0.607	0.525
	F*	B	0.493	0.422-0.556	0.497	0.430-0.562	0.512	0.422-0.600	0.495	0.415-0.575	0.503
Models developed from RNA-Seq	A*	A	0.655	0.456-0.759	0.653	0.528-0.752	0.695	0.610-0.747	0.656	0.586-0.714	0.665
	A*	B	0.551	0.367-0.719	0.572	0.421-0.705	0.692	0.614-0.747	0.651	0.575-0.710	0.584
	B*	A	0.778	0.715-0.811	0.571	0.516-0.636	0.776	0.735-0.815	0.641	0.583-0.704	0.777
	B*	B	0.740	0.524-0.807	0.643	0.500-0.768	0.775	0.723-0.815	0.629	0.556-0.698	0.746
	C*	A	0.991	0.979-0.992	0.991	0.981-0.992	0.992	0.992-0.992	0.991	0.992-0.992	0.991
	C*	B	0.797	0.797-0.801	0.823	0.822-0.826	0.987	0.979-0.992	0.987	0.981-0.992	0.796
	D*	A	0.862	0.651-0.956	0.832	0.632-0.945	0.914	0.846-0.956	0.896	0.809-0.946	0.863
	D*	B	0.781	0.408-0.941	0.812	0.548-0.937	0.910	0.824-0.956	0.890	0.782-0.946	0.775
	E*	A	0.538	0.333-0.689	0.546	0.452-0.632	0.606	0.478-0.706	0.526	0.432-0.618	0.560
	E*	B	0.607	0.400-0.722	0.502	0.420-0.609	0.593	0.500-0.689	0.511	0.419-0.615	0.603
	F*	A	0.491	0.411-0.584	0.500	0.421-0.588	0.497	0.405-0.589	0.495	0.401-0.588	0.494
	F*	B	0538	0.456-0.600	0.505	0.440-0585	0.492	0.411-0.567	0.502	0.424-0.574	0.516

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