A comparative assessment on gene expression classification methods of RNA-seq data generated using next-generation sequencing (NGS)

Abstract

Next-generation sequencing or massively parallel sequencing have revolutionized genomic research. RNA sequencing (RNA-Seq) can profile the gene-expression used for molecular diagnosis, disease classification and providing potential markers of diseases. For classification of gene expressions, several methods that have been proposed are based on microarray data which is a continuous scale or require a normal distribution assumption. As the RNA-Seq data do not meet those requirements, these methods cannot be applied directly. In this study, we compare several classifiers including Logistic Regression, Support Vector Machine, Classification and Regression Trees and Random Forest. A simulation study with different parameters such as over dispersion, differential expression rate is conducted and the results are compared with two mRNA experimental datasets. To measure predictive accuracy six performance indicators are used: Percentage Correctly Classified, Area Under Receiver Operating Characteristic (ROC) Curve, Kolmogorov Smirnov Statistics, Partial Gini Index, H-measure and Brier Score. The result shows that Random Forest outperforms the other classification algorithms.