A method for analyzing a cluster of microarray data including missing values and a program storage medium thereof are provided to solve a problem not applied to cluster analysis caused from impossibility for calculating a distance between genes in case that the missing values are present in the cluster analysis and to utilize all gene information of the microarray data by including the gene having the missing values to the cluster analysis. The number of microarray data clusters is determined(S100). The cluster analysis for each sample is performed by using a cluster analysis algorithm based on the fixed number of microarray data clusters(S200). Similar clusters among all samples are determined for the fixed cluster of each sample(S300). The cluster of each gene is determined by combining the clusters identifiable through the similar cluster(S400).
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