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The objectives of this study were: (1) to estimate relative magnitudes of different sources of variation and (2) to evaluate agreement between biological and technical replicates.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We performed a microarray experiment using a total of 24 Affymetrix GeneChip<jats:sup>\u00ae<\/jats:sup>arrays. The study included 4<jats:sup>th<\/jats:sup>mammary gland samples from eight 21-day-old<jats:italic>Sprague Dawley CD<\/jats:italic>female rats exposed to genistein (soy isoflavone). RNA samples from each rat were split to assess variation arising at labeling and hybridization steps. A general linear model was used to estimate variance components. Pearson correlations were computed to evaluate agreement between technical and biological replicates.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The greatest source of variation was biological variation, followed by residual error, and finally variation due to labeling when *.cel files were processed with dChip and RMA image processing algorithms. When MAS 5.0 or GCRMA-EB were used, the greatest source of variation was residual error, followed by biology and labeling. 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