Random Forest in Clinical Metabolomics for Phenotypic Discrimination and Biomarker Selection

Table 2

Averaged error rates and their standard deviations of RF, PLS, LDA, and SVM on 2 cases by 7- and 10-fold cross-validation as well as 10% and 15% hold out cross-validation (100 times).

Case	Evaluation item	RF error rate		PLS error rate		SVM error rate		LDA error rate
		mean (S.D.)		mean (S.D.)		mean (S.D.)		mean (S.D.)
(A) Normal versus CRC	7-fold CV	0.071	(8.364𝐸−03)	0.134	(7.845𝐸−02)	0.148	(7.998𝐸−02)	0.227	(9.897𝐸−02)
	10-fold CV	0.069	(7.482𝐸−03)	0.094	(8.990𝐸−02)	0.126	(6.673𝐸−02)	0.188	(1.375𝐸−01)
	15% holdout CV	0.065	(6.545𝐸−03)	0.132	(7.009𝐸−02)	0.117	(7.344𝐸−02)	0.189	(8.206𝐸−02)
	10% holdout CV	0.065	(5.445𝐸−03)	0.121	(8.407𝐸−02)	0.113	(8.572𝐸−02)	0.181	(1.073𝐸−01)
(B) Pre versus post	7-fold CV	0.102	(3.687𝐸−03)	0.130	(7.321𝐸−02)	0.170	(8.069𝐸−02)	0.108	(5.517𝐸−02)
	10-fold CV	0.096	(3.954𝐸−03)	0.169	(1.242𝐸−01)	0.163	(1.524𝐸−01)	0.096	(1.069𝐸−01)
	15% holdout CV	0.088	(3.592𝐸−03)	0.137	(6.687𝐸−02)	0.186	(8.412𝐸−02)	0.127	(7.958𝐸−02)
	10% holdout CV	0.083	(3.188𝐸−03)	0.145	(9.883𝐸−02)	0.161	(8.644𝐸−02)	0.114	(9.375𝐸−02)