Jianhua Hu1, Fei Zou, Fred A Wright. 1. Department of Biostatistics and Applied Mathematics, University of Texas M.D. Anderson Cancer Center, TX 77030-4009, USA. jhu@mdanderson.org
Abstract
MOTIVATION: Owing to the experimental cost and difficulty in obtaining biological materials, it is essential to consider appropriate sample sizes in microarray studies. With the growing use of the False Discovery Rate (FDR) in microarray analysis, an FDR-based sample size calculation is essential. METHOD: We describe an approach to explicitly connect the sample size to the FDR and the number of differentially expressed genes to be detected. The method fits parametric models for degree of differential expression using the Expectation-Maximization algorithm. RESULTS: The applicability of the method is illustrated with simulations and studies of a lung microarray dataset. We propose to use a small training set or published data from relevant biological settings to calculate the sample size of an experiment. AVAILABILITY: Code to implement the method in the statistical package R is available from the authors.
MOTIVATION: Owing to the experimental cost and difficulty in obtaining biological materials, it is essential to consider appropriate sample sizes in microarray studies. With the growing use of the False Discovery Rate (FDR) in microarray analysis, an FDR-based sample size calculation is essential. METHOD: We describe an approach to explicitly connect the sample size to the FDR and the number of differentially expressed genes to be detected. The method fits parametric models for degree of differential expression using the Expectation-Maximization algorithm. RESULTS: The applicability of the method is illustrated with simulations and studies of a lung microarray dataset. We propose to use a small training set or published data from relevant biological settings to calculate the sample size of an experiment. AVAILABILITY: Code to implement the method in the statistical package R is available from the authors.
Authors: Takafumi Sangai; Argun Akcakanat; Huiqin Chen; Emily Tarco; Yun Wu; Kim-Anh Do; Todd W Miller; Carlos L Arteaga; Gordon B Mills; Ana Maria Gonzalez-Angulo; Funda Meric-Bernstam Journal: Clin Cancer Res Date: 2012-08-29 Impact factor: 12.531
Authors: Howard B Gutstein; Jeffrey S Morris; Suresh P Annangudi; Jonathan V Sweedler Journal: Mass Spectrom Rev Date: 2008 Jul-Aug Impact factor: 10.946