Frontiers of Computer Science: Selected Publications from Chinese Universities
A new gene selection method for microarray data based on PSO and informativeness metric
ICIC'13 Proceedings of the 9th international conference on Intelligent Computing Theories and Technology
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Motivation: Unsupervised ‘cluster’ analysis is an invaluable tool for exploratory microarray data analysis, as it organizes the data into groups of genes or samples in which the elements share common patterns. Once the data are clustered, finding the optimal number of informative subgroups within a dataset is a problem that, while important for understanding the underlying phenotypes, is one for which there is no robust, widely accepted solution. Results: To address this problem we developed an ‘informativeness metric’ based on a simple analysis of variance statistic that identifies the number of clusters which best separate phenotypic groups. The performance of the informativeness metric has been tested on both experimental and simulated datasets, and we contrast these results with those obtained using alternative methods such as the gap statistic. Availability: The method has been implemented in the Bioconductor R package attract; it is also freely available from http://compbio.dfci.harvard.edu/pubs/attract_1.0.1.zip. Contact:jess@jimmy.harvard.edu; johnq@jimmy.harvard.edu Supplementary information:Supplementary data are available at Bioinformatics online.