Combining LPP with PCA for microarray data clustering

DNA microarray technique has produced large amount of gene expression data. To analyze these data, many excellent machine learning techniques have been proposed in recent related work. In this paper, we try to perform the clustering of microarray data by combining the recently proposed locality preserving projection (LPP) method with PCA, i.e. PCA-LPP. The comparison between PCA and PCA-LPP is performed based on two clustering algorithms, K-means and agglomerative hierarchical clustering. As we already known, clustering with the components extracted by PCA instead of the original variables does improve cluster quality. Moreover, our empirical study shows that by using LPP to perform further process the dimensions of components extracted by PCA can be further reduced and the quality of the clusters can be improved greatly meanwhile. Particularly, the first few components obtained by PCA-LPP capture more information of the cluster structure than those of PCA.