title: Statistical methodology for the analysis of dye-switch microarray experiments.
abstract: BACKGROUND
  In individually dye-balanced microarray designs, each biological sample is hybridized on two different slides, once with Cy3 and once with Cy5. While this strategy ensures an automatic correction of the gene-specific labelling bias, it also induces dependencies between log-ratio measurements that must be taken into account in the statistical analysis.
  
  
  RESULTS
  We present two original statistical procedures for the statistical analysis of individually balanced designs. These procedures are compared with the usual ML and REML mixed model procedures proposed in most statistical toolboxes, on both simulated and real data.
  
  
  CONCLUSIONS
  The UP procedure we propose as an alternative to usual mixed model procedures is more efficient and significantly faster to compute. This result provides some useful guidelines for the analysis of complex designs.
authors.affiliation: UMR AgroParisTech/INRA 518, 16, rue Claude Bernard 75231 Paris CEDEX 05, France. maryhuar@agroparistech.fr
authors.forename: Tristan
authors.initials: T
authors.lastname: Mary-Huard
authors.forename: Julie
authors.initials: J
authors.lastname: Aubert
authors.forename: Nadera
authors.initials: N
authors.lastname: Mansouri-Attia
authors.forename: Olivier
authors.initials: O
authors.lastname: Sandra
authors.forename: Jean-Jacques
authors.initials: JJ
authors.lastname: Daudin
mesh_terms: D000465:Algorithms; D003627:Data Interpretation, Statistical; D005456:Fluorescent Dyes; D020869:Gene Expression Profiling / 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
chemical_list: D005456:Fluorescent Dyes