Preprocessing implementation for microarray (PRIM): an efficient method for processing cDNA microarray data

cDNA microarray technology is useful for systematically analyzing the expre ssion 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 sti ll questions about the reproducibility of the data. We have therefore devel oped a data processing method that very efficiently extracts reproducible d ata from the result of duplicate experiments. It is designed to automatical ly filter the raw results obtained from cDNA microarray image-analysis soft ware. We optimize the threshold value for filtering the data by using the p roduct 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 coeff icient for results obtained in the duplicate experiments. Using this method to process mouse tissue expression profile data that contain 1,881,600 poi nts of analysis, we obtained clustered results more reasonable than those o btained using previously reported filtering methods.