Feature selection is one of the most important research topics in high dimensional array data analysis. We propose a two-way filtering based method that utilizes a pair of statistics coupled with rigorous cross-validation to identify the most informative features from different types of distributions. We evaluate the utility of the proposed adaptive feature selection method on six MicroArray Quality Control Phase II (MAQC-II) datasets. The results show that our method yields models with significantly fewer features and can achieve comparable or superior classification performance compared to models generated from other feature selection methods, suggesting high quality feature selection.

SUMMARY: This synopsis provides an overview of array-based comparative genomic hybridization data display, abstraction and analysis using CGHAnalyzer, a software suite, designed specifically for this purpose. CGHAnalyzer can be used to simultaneously load copy number data from multiple platforms, query and describe large, heterogeneous datasets and export results. Additionally, CGHAnalyzer employs a host of algorithms for microarray analysis that include hierarchical clustering and class differentiation. AVAILABILITY: CGHAnalyzer, the accompanying manual, documentation and sample data are available for download at http://acgh.afcri.upenn.edu. This is a Java-based application built in the framework of the TIGR MeV that can run on Microsoft Windows, Macintosh OSX and a variety of Unix-based platforms. It requires the installation of the free Java Runtime Environment 1.4.1 (or more recent) (http://www.java.sun.com).