Random Forest in Clinical Metabolomics for Phenotypic Discrimination and Biomarker Selection

• Published in: Evidence-based complementary and alternative medicine Vol. 2013; no. 2013; pp. 1 - 11
• Main Authors: Zhao, Aihua, Wang, Congrong, Bao, Yu-Qian, Jia, Weiping, Liu, Jiajian, Zhang, Yinan, Chen, Tianlu, Cao, Yu
• Format: Journal Article
• Language: English
• Published: Cairo, Egypt Hindawi Puplishing Corporation 01.01.2013; Hindawi Publishing Corporation; John Wiley & Sons, Inc
• Subjects: Arthritis; Artificial intelligence; Bioinformatics; Biomarkers; Chromatography; Classification; Colorectal cancer; Colorectal carcinoma; Data analysis; Data processing; Datasets; Gas chromatography; Gene expression; Genetic diversity; Mass spectrometry; Mass spectroscopy; Metabolism; Metabolites; Metabolomics; NMR; Nuclear magnetic resonance; Oral cancer; Principal components analysis; Proteomics; Scientific imaging; Statistical analysis; Urine; Variance analysis
• ISSN: 1741-427X; 1741-4288; 1741-4288
• DOI: 10.1155/2013/298183

Metabolomic data analysis becomes increasingly challenging when dealing with clinical samples with diverse demographic and genetic backgrounds and various pathological conditions or treatments. Although many classification tools, such as projection to latent structures (PLS), support vector machine (SVM), linear discriminant analysis (LDA), and random forest (RF), have been successfully used in metabolomics, their performance including strengths and limitations in clinical data analysis has not been clear to researchers due to the lack of systematic evaluation of these tools. In this paper we comparatively evaluated the four classifiers, PLS, SVM, LDA, and RF, in the analysis of clinical metabolomic data derived from gas chromatography mass spectrometry platform of healthy subjects and patients diagnosed with colorectal cancer, where cross-validation, R2/Q2 plot, receiver operating characteristic curve, variable reduction, and Pearson correlation were performed. RF outperforms the other three classifiers in the given clinical data sets, highlighting its comparative advantages as a suitable classification and biomarker selection tool for clinical metabolomic data analysis.