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PubMed · 15151695

Spotting effect in microarray experiments.

Tristan Mary-Huard·Jean-Jacques Daudin·Stéphane Robin·Frédérique Bitton·Eric Cabannes·Pierre Hilson
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Abstract

BACKGROUND: Microarray data must be normalized because they suffer from multiple biases. We have identified a source of spatial experimental variability that significantly affects data obtained with Cy3/Cy5 spotted glass arrays. It yields a periodic pattern altering both signal (Cy3/Cy5 ratio) and intensity across the array. RESULTS: Using the variogram, a geostatistical tool, we characterized the observed variability, called here the spotting effect because it most probably arises during steps in the array printing procedure. CONCLUSIONS: The spotting effect is not appropriately corrected by current normalization methods, even by those addressing spatial variability. Importantly, the spotting effect may alter differential and clustering analysis.

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AnimalsArabidopsisDNA, ComplementaryDNA, PlantDNA, ProtozoanDatabases, GeneticGene Expression ProfilingGene Expression RegulationGene Expression Regulation, PlantNormal DistributionOligonucleotide Array Sequence AnalysisPlasmodium falciparumResearch DesignComparative StudyJournal ArticleResearch Support, Non-U.S. Gov't

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Tristan Mary-Huard, Jean-Jacques Daudin, Stéphane Robin, Frédérique Bitton, Eric Cabannes, Pierre Hilson. 2004-05-19. Spotting effect in microarray experiments.. https://doi.org/10.1186/1471-2105-5-63

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