Clustering technique is one of the useful tools to elucidate similar patterns across large number of transcripts and to identify likely co-regulated genes. It attempts to partition the genes into groups exhibiting similar patterns of variation in expression level. An application of rough-fuzzy c-means (RFCM) algorithm is presented in this paper to discover co-expressed gene clusters. Selection of initial prototypes of different clusters is one of the major issues of the RFCM based microarray data clustering. The pearson correlation based initialization method is used to address this limitation. It enables the RFCM algorithm to discover co-expressed gene clusters. The effectiveness of the RFCM algorithm and the initialization method, along with a comparison with other related methods, is demonstrated on five yeast gene expression data sets using standard cluster validity indices and gene ontology based analysis. © 2012 Springer-Verlag.