Semiparametric clustering method for microarray data analysis.
Clustering is a major tool for microarray gene expression data analysis. The existing clustering methods fall mainly into two categories: parametric and nonparametric. The parametric methods generally assume a mixture of parametric subdistributions. When the mixture distribution approximately fits the true data generating mechanism, the parametric methods perform well, but not so when there is nonnegligible deviation between them. On the other hand, the nonparametric methods, which usually do not make distributional assumptions, are robust but pay the price for efficiency loss. In an attempt to utilize the known mixture form to increase efficiency, and to free assumptions about the unknown subdistributions to enhance robustness, we propose a semiparametric method for clustering. The proposed approach possesses the form of parametric mixture, with no assumptions to the subdistributions. The subdistributions are estimated nonparametrically, with constraints just being imposed on the modes. An expectation-maximization (EM) algorithm along with a classification step is invoked to cluster the data, and a modified Bayesian information criterion (BIC) is employed to guide the determination of the optimal number of clusters. Simulation studies are conducted to assess the performance and the robustness of the proposed method. The results show that the proposed method yields reasonable partition of the data. As an illustration, the proposed method is applied to a real microarray data set to cluster genes.
Yuan
Ao
A
National Human Genome Center, Department of Community Health and Family Medicine, Howard University, Washington, DC, USA. yuanao@hotmail.com
He
Wenqing
W
D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D003627:Data Interpretation, Statistical; D006801:Humans; D046228:Microarray Analysis / Q000379:methods*; D018709:Statistics, Nonparametric