title: Expression ratio evaluation in two-colour microarray experiments is significantly improved by correcting image misalignment.
abstract: 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/.
authors: Centre de Génétique Moléculaire, CNRS UPR2167 and Gif/Orsay DNA MicroArray Platform (GODMAP), 91190 Gif-sur-Yvette, France. tang@cgm.cnrs-gif.fr
authors: Thomas
authors: T
authors: Tang
authors: Nicolas
authors: N
authors: François
authors: Annie
authors: A
authors: Glatigny
authors: Nicolas
authors: N
authors: Agier
authors: Marie-Hélène
authors: MH
authors: Mucchielli
authors: Lawrence
authors: L
authors: Aggerbeck
authors: Hervé
authors: H
authors: Delacroix
mesh_terms: 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