Microarrays Commons^™

The Optimal Confidence Region For A Random Parameter, Hajime Uno, Lu Tian, L.J. Wei

Harvard University Biostatistics Working Paper Series

Under a two-level hierarchical model, suppose that the distribution of the random parameter is known or can be estimated well. Data are generated via a fixed, but unobservable realization of this parameter. In this paper, we derive the smallest confidence region of the random parameter under a joint Bayesian/frequentist paradigm. On average this optimal region can be much smaller than the corresponding Bayesian highest posterior density region. The new estimation procedure is appealing when one deals with data generated under a highly parallel structure, for example, data from a trial with a large number of clinical centers involved or genome-wide …

A Model Based Background Adjustment For Oligonucleotide Expression Arrays, Zhijin Wu, Rafael A. Irizarry, Robert Gentleman, Francisco Martinez Murillo, Forrest Spencer

Johns Hopkins University, Dept. of Biostatistics Working Papers

High density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of further pre-processing and data reduction occurs following the image processing step. Statistical procedures developed by academic groups have been successful at improving the default algorithms provided by the Affymetrix system. In this paper we present a solution to one of the pre-processing steps, background adjustment, based on a formal statistical framework. Our solution greatly improves the performance of the technology in various practical applications.

Affymetrix GeneChip arrays use short oligonucleotides to …