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Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays

Jeffrey P Townsend

Author Affiliations

Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA

BMC Bioinformatics 2004, 5:54  doi:10.1186/1471-2105-5-54

Published: 5 May 2004

Abstract

Background

The detection of small yet statistically significant differences in gene expression in spotted DNA microarray studies is an ongoing challenge. Meeting this challenge requires careful examination of the performance of a range of statistical models, as well as empirical examination of the effect of replication on the power to resolve these differences.

Results

New models are derived and software is developed for the analysis of microarray ratio data. These models incorporate multiplicative small error terms, and error standard deviations that are proportional to expression level. The fastest and most powerful method incorporates additive small error terms and error standard deviations proportional to expression level. Data from four studies are profiled for the degree to which they reveal statistically significant differences in gene expression. The gene expression level at which there is an empirical 50% probability of a significant call is presented as a summary statistic for the power to detect small differences in gene expression.

Conclusions

Understanding the resolution of difference in gene expression that is detectable as significant is a vital component of experimental design and evaluation. These small differences in gene expression level are readily detected with a Bayesian analysis of gene expression level that has additive error terms and constrains samples to have a common error coefficient of variation. The power to detect small differences in a study may then be determined by logistic regression.