Some aspects of the design and analysis of gene expression microarray experiments
by
Yee Hwa Yang
Department of Statistics, University of California, Berkeley
Coauthors: Terence P. Speed

The objective of experimental design is to make the analysis of data and the interpretation of the results as simple and powerful as possible, while keeping the purpose of the experiment and the constraints of the experimental material clearly in mind. In cDNA microarray experiments, a popular design choice is to use a common reference sample in every experiment. This approach provides an easy means of comparing multiple samples against one another, as well as permitting the combination of results from different experiments. We will show in theory and with experimental data that the common reference approach is inherently more variable than direct comparison. Furthermore, we demonstrate that in the absence of any common reference, combining different sets of experimental data can be done efficiently by performing A-optimal linked hybridizations between these sets of experiments. We will also describe different questions we have met and the experimental designs and analysis we have used to answer these questions. Experiments and data concerning the mouse olfactory system will be used to demonstrate our methods for analyzing multilevel factorial (including spatial and temporal) experiments.

Date received: August 31, 2001