An Iterative Nonlinear Regression Method for Microarray Data Normalization

ABSTRACT

Normalization is a prerequisite for almost all follow-up steps in microarray data analysis. Accurate normalization across different experiments and phenotypes assures a common base for comparative yet quantitative studies using gene expression data. In this paper, we report a novel normalization approach, namely iterative nonlinear regression (INR) method, which exploits concurrent identification of invariantly expressed genes (IEGs) and implementation of nonlinear regression normalization. The INR scheme features an iterative process that performs the following two steps alternatively: (1) selection of IEGs and (2) estimation of nonlinear regression function for normalization. We demonstrate the principle and performance of the INR approach on two real microarray data sets. As compared to major peer methods (e.g., linear regression method, Loess method and iterative ranking method), INR method shows an improved performance in achieving low expression variance across replicates and excellent fold-change preservation for differently expressed genes.