Gene expression profile class prediction using linear Bayesian classifiers

Abstract

Due to recent advances in DNA microarray technology using gene expression profiles diagnostic category of tissue samples can be predicted with high accuracy. In this study we discuss shortcomings of some existing gene expression profile classification methods and propose a new approach based on linear Bayesian classifiers. In our approach we first construct gene-level linear classifiers to identify genes that provide high class-prediction accuracies i.e. low error rates. After this screening phase starting with the gene that offers the lowest error rate we construct a multi-dimensional linear classifier by incorporating next best-per-forming genes until the prediction error becomes minimum or 0 if possible. When we compared classification performance of our approach against prediction analysis of microarrays (PAM) and support vector machines (SVM) based approaches we found that our method outperforms PAM and produces comparable results with SVM. In addition we observed that the gene selection scheme of PAM could be misleading. Albeit SVM achieves relatively higher prediction performance it has two major disadvantages: Complexity and lack of insight about important genes. Our intuitive approach offers competing performance and also an efficient means for finding important genes. (c) 2007 Elsevier Ltd. All rights reserved.