A Comparison of Parametric and Semi-Parametric Models for Microarray Data Analysis

Microarray technology has revolutionized genomic studies by enabling the study of differential expression of thousands of genes simultaneously. Parametric, nonparametric and semi-parametric statistical methods have been proposed for gene selection within the last sixteen years. In an effort to find the “gold standard", the performance of some common parametric and nonparametric methods have been compared in terms of power to select differentially expressed genes and other desirable properties. However, no such comparisons have been conducted between parametric and semi-parametric models. In this study, we compared a semi-parametric model based on copulas with a parametric model (the quantitative trait analysis or QTA model) in terms of power and the ability to control the Type I error rate. In addition, we proposed a simple algorithm for choosing an optimal copula. The two approaches were applied to a publicly available melanoma cell lines dataset for validation. Both methods performed well in terms of power but the copula approach was notably the better. In terms of the Type I error rate control, the two methods were comparable. More methods for selecting an optimal copula for gene expression data need to be developed, as the proposed procedure is limited to copulas that permit both negative and positive dependence only.

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