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Bioinformatics Advance Access published online on August 12, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm399
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Expression ratio evaluation in two-colour microarray experimentsis significantly improved by correcting image mis-alignment

Thomas Tang 1,2,*, Nicolas François 1, Annie Glatigny 1, Nicolas Agier 1, Marie-Hélène Mucchielli 1,2, Lawrence Aggerbeck 1 and Hervé Delacroix 1,3

1Centre de Génétique Moléculaire, CNRS UPR2167 and Gif/Orsay DNA MicroArray Platform (GODMAP), 91190 Gif-sur-Yvette, France
2Université Pierre et Marie Curie - Paris 6, 75005 Paris, France
3Université Paris-Sud - Paris 11, 91405 Orsay, France

*To whom correspondence should be addressed. Thomas Tang, E-mail: tang{at}cgm.cnrs-gif.fr


  Abstract

Motivation: Two-colour microarrays are widely used to perform transcriptome analysis. In most cases, it appears that the "red" and "green" images resulting from the scan of a microarray slide are slightly shifted one with respect to the other. To increase the robust-ness of the measurement of the fluorescent emission intensities, multiple acquisitions with the same or different PMT gains can be used. In these cases, a systematic correction of image shift is re-quired.

Results: To accurately detect this shift, we first developed an ap-proach using cross-correlation. Secondly, we evaluated the most appropriate interpolation method to be used to derive the registered image. Then, we quantified the effects of image shifts on spot qual-ity, using two different quality estimators. Finally, we measured the benefits associated with a systematic image registration. In this study, we demonstrate that registering the two images prior to data extraction provides a more reliable estimate of the two colours’ ratio and thus increases the accuracy of measurements of variations in gene expression.

Availability: http://bioinfome.cgm.cnrs-gif.fr/

Contact: tang{at}cgm.cnrs-gif.fr

Associate Editor: Prof. David Rocke

Received on June 13, 2007; revised on July 26, 2007; accepted on August 2, 2007

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