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Open Access Method

Exploratory differential gene expression analysis in microarray experiments with no or limited replication

Alexander V Loguinov1*, I Saira Mian2 and Chris D Vulpe1*

Author Affiliations

1 Department of Nutritional Sciences and Toxicology, University of California at Berkeley, Morgan Hall, Berkeley, CA 94720, USA

2 Life Sciences Division, Lawrence Berkeley National Laboratory, Cyclotron Road, Berkeley, CA 94720, USA

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Genome Biology 2004, 5:R18  doi:10.1186/gb-2004-5-3-r18

Published: 1 March 2004

Abstract

We describe an exploratory, data-oriented approach for identifying candidates for differential gene expression in cDNA microarray experiments in terms of α-outliers and outlier regions, using simultaneous tolerance intervals relative to the line of equivalence (Cy5 = Cy3). We demonstrate the improved performance of our approach over existing single-slide methods using public datasets and simulation studies.