A censored beta mixture model for the estimation of the proportion of non-differentially expressed genes.
BACKGROUND
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.


BACKGROUND
The R code is freely available at http://home.gwu.edu/~ylai/research/CBpi0/.
Markitsis
Anastasios
A
Department of Statistics, The George Washington University, Washington, DC 20052, USA.
Lai
Yinglei
Y
D003198:Computer Simulation; D030541:Databases, Genetic; D005189:False Positive Reactions; D020869:Gene Expression Profiling / Q000379:methods*; D015233:Models, Statistical