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BMC Bioinformatics

, 5:63

First Online: 19 May 2004Received: 09 January 2004Accepted: 19 May 2004


BackgroundMicroarray 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.

ResultsUsing 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.

ConclusionsThe 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.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2105-5-63 contains supplementary material, which is available to authorized users.

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Autor: Tristan Mary-Huard - Jean-Jacques Daudin - Stéphane Robin - Frédérique Bitton - Eric Cabannes - Pierre Hilson


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