Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment.
BACKGROUND
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 robustness 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 required.


RESULTS
To accurately detect this shift, we first developed an approach using cross-correlation. Second, 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 quality, 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.


BACKGROUND
http://bioinfome.cgm.cnrs-gif.fr/.
Tang
Thomas
T
Centre de Génétique Moléculaire, CNRS UPR2167 and Gif/Orsay DNA MicroArray Platform (GODMAP), 91190 Gif-sur-Yvette, France. tang@cgm.cnrs-gif.fr
François
Nicolas
N
Glatigny
Annie
A
Agier
Nicolas
N
Mucchielli
Marie-Hélène
MH
Aggerbeck
Lawrence
L
Delacroix
Hervé
H
D016477:Artifacts; D007089:Image Enhancement / Q000379:methods*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D036641:Microscopy, Fluorescence, Multiphoton / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity