Anastasios Markitsis1, Yinglei Lai. 1. Department of Statistics, The George Washington University, Washington, DC 20052, USA.
Abstract
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/.
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/.
Authors: Dinesh Singh; Phillip G Febbo; Kenneth Ross; Donald G Jackson; Judith Manola; Christine Ladd; Pablo Tamayo; Andrew A Renshaw; Anthony V D'Amico; Jerome P Richie; Eric S Lander; Massimo Loda; Philip W Kantoff; Todd R Golub; William R Sellers Journal: Cancer Cell Date: 2002-03 Impact factor: 31.743
Authors: Vamsi K Mootha; Cecilia M Lindgren; Karl-Fredrik Eriksson; Aravind Subramanian; Smita Sihag; Joseph Lehar; Pere Puigserver; Emma Carlsson; Martin Ridderstråle; Esa Laurila; Nicholas Houstis; Mark J Daly; Nick Patterson; Jill P Mesirov; Todd R Golub; Pablo Tamayo; Bruce Spiegelman; Eric S Lander; Joel N Hirschhorn; David Altshuler; Leif C Groop Journal: Nat Genet Date: 2003-07 Impact factor: 38.330