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1 Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center, RIKEN Yokahama Institute, Yokohama City, Kanagawa 230-0045, Japan
2 Department of Biotechnology, University of Tokyo, Tokyo 113-8657, Japan
3 Core Research for Evolutional Science and Technology, Japan Science and Technology Corporation, Ibaraki 305-0074
4 Cooperative Graduate School of Medicine, Tsukuba University, Ibaraki 305-8575, Japan
cDNA microarray technology is useful for systematically analyzing the expression profiles of thousands of genes at once. Although many useful results inferred by using this technology and a hierarchical clustering method for statistical analysis have been confirmed using other methods, there are still questions about the reproducibility of the data. We have therefore developed a data processing method that very efficiently extracts reproducible data from the result of duplicate experiments. It is designed to automatically filter the raw results obtained from cDNA microarray image-analysis software. We optimize the threshold value for filtering the data by using the product of N and R, where N is the ratio of the number of spots that passed the filtering vs. the total number of spots, and R is the correlation coefficient for results obtained in the duplicate experiments. Using this method to process mouse tissue expression profile data that contain 1,881,600 points of analysis, we obtained clustered results more reasonable than those obtained using previously reported filtering methods.
expression profiling; data processing; cluster analysis
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