Motivation: The proportion of non-differentially expressed genes (pi(0)) is an important quantity in microarray data analysis. Although many statistical methods have been proposed for its estimation, it is still necessary to develop more efficient methods.
Methods: Our approach for improving pi(0) estimation is to modify an existing simple method by introducing artificial censoring to P-values. In a comprehensive simulation study and the applications to experimental datasets, we compare our method with eight existing estimation methods.
Results: The simulation study confirms that our method can clearly improve the estimation performance. Compared with the existing methods, our method can generally provide a relatively accurate estimate with relatively small variance. Using experimental microarray datasets, we also demonstrate that our method can generally provide satisfactory estimates in practice.
Availability: The R code is freely available at http://home.gwu.edu/~ylai/research/CBpi0/.