Abstract: Common ratio-based approaches for analyzing gene expression microarray data do not provide a framework for handling replication, although replication is clearly desirable for these noisy data. In contrast, replication fits naturally into analysis of variance (ANOVA) methods. We use ANOVA to analyze data from a microarray experiment to compare gene expression in drug-treated and control cells lines. We discuss issues that commonly arise in the analysis of microarray data, and present practical solutions to some common problems.
Key words and phrases: Analysis of variance, bootstrap, cDNA microarray, gene expression, orthogonal design.