Jane Chang
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Russell D. Wolfinger
David Allison
Jenny Bryan
Lai-Har Chi
Jane Chang
Philip Dixon
Kent M. Eskridge
Deborah Glueck
David L. Gold
Susan G. Hilsenbeck
Lawrence Hunter
Rebecka Jornsten
Steen Knudsen
Laura Lazzeroni
Chen-Tuo Liao
Peter Munson
Dan Nettleton
Wei Pan
David M. Rocke
Grace S. Shieh
Lue Ping Zhao
Deepak Mav
Annette Molinaro

Design and Analysis of 2-Channel Microarry Experiments

Jane Chang, Dept. of Applied Statistics and Operations Research Bowling Green State University, Jason Hsu and Tao Wang of The Ohio State University

In this research, we provide an integrated environment for designing and analyzing gene expression data from 2-channel microarrays, from design of the arrays with sample size computation, to exact multiplicity-adjusted inference for differential gene expressions. There are two possible formulations to the comparison of gene expression levels: tests of equality and confidence intervals. The testing formulation has been more popular, but confidence intervals are more informative because they not only infer the existence of differential expressions, but also bound the magnitude of such differentials. We provide simultaneous confidence intervals. Before gene expression levels can be compared, the data need to be pre-processed to adjust for variations in the arrays, and unequal affinity of genes to dyes. Processed data are then normalized with respect to control genes (which may be all the target genes or a set of housekeeping genes). The approach we take is to model the data. Pre-processing to adjust for array and dye differences amounts to fitting array and dye effects and gene x dye interaction in the model. Choosing what genes to normalize with specifies a set of estimable functions as the normalized expression differentials. The correlation stucture of estimates of these functions can then be derived based on the model, allowing accuate multiplicity adjustment to obtain simultaneous confidence intervals.

Graybill Conference
June 18-20, 2003
University Park Holiday Inn
Fort Collins, CO 80526
email: hari@stat.colostate.edu Fax: (970)491-7895 Phone: (970)491-5269
Last Updated: Wednesday, April 16, 2003