The retrieved documents have to be transformed into proper data structure for the clustering algorithms of statistics and machine learning. A popular data structure for document clustering is document-term matrix. This matrix has the occurred frequency value of a term in each document. There is a sparsity problem in this matrix because most frequencies of the matrix are 0 values. This problem affects the clustering performance. The sparseness of document-term matrix decreases the performance of clustering result. So, this research uses the factor score by factor analysis to solve the sparsity problem in document clustering. The document-term matrix is transformed to document-factor score matrix using factor scores in this paper. Also, the document-factor score matrix is used as input data for document clustering. To compare the clustering performances between document-term matrix and document-factor score matrix, this research applies two typed matrices to self organizing map (SOM) clustering.