Random forest for gene selection and microarray data classification

Abstract

A random forest method has been selected to perform both gene selection and classification of the microarray data. The goal of this research is to develop and improve the random forest gene selection method. Hence, improved gene selection method using random forest has been proposed to obtain the smallest subset of genes as well as biggest subset of genes prior to classification. In this research, ten datasets that consists of different classes are used, which are Adenocarcinoma, Brain, Breast (Class 2 and 3), Colon, Leukemia, Lymphoma, NCI60, Prostate and Small Round Blue-Cell Tumor (SRBCT). Enhanced random forest gene selection has performed better in terms of selecting the smallest subset as well as biggest subset of informative genes through gene selection. Furthermore, the classification performed on the selected subset of genes using random forest has lead to lower prediction error rates compared to existing method and other similar available methods. © 2012 Springer-Verlag.