An optimal choice of window width for LOWESS normalization of microarray data

Abstract

The purpose of normalization in microarray data analysis is to minimize systematic variations in the measured gene expression levels of two co-hybridized mRNA samples so that biological differences can be more easily distinguished. The most commonly and widely used normalization procedure for spotted arrays is probably the intensity dependent and print-tip LOWESS normalization. It is well known that the choices of different parameter values greatly affect the quality of the normalization results, and thus poor quality of the normalization results could be due to the arbitrary choice of the smoothing parameters for LOWESS normalization. In many normalization studies, however, LOWESS has been simply used without rigorous consideration of the parameters. In this article, we propose a bootstrap method to find the optimal window width in print-tip normalization by applying the cross validation technique. We also compare through simulation studies the normalization results by using the proposed method with those by fixing the window width.