A simple method for statistical analysis of intensity differences in microarray-derived gene expression data
AffiliationArcaris, Inc. (Currently Deltagen Proteomics, Inc.) Salt Lake City, UT USA
Dept of Molecular and Cell Biology and ARL Division of Neurobiology University of Arizona Tucson, AZ USA
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CitationBMC Biotechnology 2001, 1:8 http://www.biomedcentral.com/1472-6750/1/8
Rights© 2001 Kamb and Ramaswami; licensee BioMed Central Ltd. Verbatim copying and redistribution of this article are permitted in any medium for any non-commercial purpose, provided this notice is preserved along with the article's original URL.
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AbstractBACKGROUND:Microarray experiments offer a potent solution to the problem of making and comparing large numbers of gene expression measurements either in different cell types or in the same cell type under different conditions. Inferences about the biological relevance of observed changes in expression depend on the statistical significance of the changes. In lieu of many replicates with which to determine accurate intensity means and variances, reliable estimates of statistical significance remain problematic. Without such estimates, overly conservative choices for significance must be enforced.RESULTS:A simple statistical method for estimating variances from microarray control data which does not require multiple replicates is presented. Comparison of datasets from two commercial entities using this difference-averaging method demonstrates that the standard deviation of the signal scales at a level intermediate between the signal intensity and its square root. Application of the method to a dataset related to the beta-catenin pathway yields a larger number of biologically reasonable genes whose expression is altered than the ratio method.CONCLUSIONS:The difference-averaging method enables determination of variances as a function of signal intensities by averaging over the entire dataset. The method also provides a platform-independent view of important statistical properties of microarray data.
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