Abstract Microarray analysis able to monitor thousands of gene expression data, however, to elucidate the hidden patterns in the data is a complex process. These gene expression data show its imprecision, noise and vagueness due to its high dimensional properties. There are a handful of clustering algorithms have been proposed to extract the important information from the gene expression data. However, identifying the underlying biological knowledge of the data is still hard. To acknowledge these issues, clustering algorithms are used to reduce the data complexity. In this article, hybrid of agglomerative hierarchical clustering and modified k-medoids (partitional clustering) are proposed. Application of the proposed of clustering algorithms to group the genes that have similar functionality which might assist pre-processing procedures. In order to emphasize the quality of the clustering results, cluster quality index (CQI) is determined. Lung and ovary data sets used and the method retrieved a fair clustering with CQI, 0.37 and 0.48 respectively. This research contributes by avoiding biasness toward genes and provide true sense of clustering output using the advantage of hierarchical and partitional clustering methods.