title: Experimental design for three-color and four-color gene expression microarrays.
abstract: BACKGROUND
  Three-color microarrays, compared with two-color microarrays, can increase design efficiency and power to detect differential expression without additional samples and arrays. Furthermore, three-color microarray technology is currently available at a reasonable cost. Despite the potential advantages, clear guidelines for designing and analyzing three-color experiments do not exist.
  
  
  RESULTS
  We propose a three- and a four-color cyclic design (loop) and a complementary graphical representation to help design experiments that are balanced, efficient and robust to hybridization failures. In theory, three-color loop designs are more efficient than two-color loop designs. Experiments using both two- and three-color platforms were performed in parallel and their outputs were analyzed using linear mixed model analysis in R/MAANOVA. These results demonstrate that three-color experiments using the same number of samples (and fewer arrays) will perform as efficiently as two-color experiments. The improved efficiency of the design is somewhat offset by a reduced dynamic range and increased variability in the three-color experimental system. This result suggests that, with minor technological improvements, three-color microarrays using loop designs could detect differential expression more efficiently than two-color loop designs.
  
  
  BACKGROUND
  http://www.jax.org/staff/churchill/labsite/software
  
  
  BACKGROUND
  Multicolor cyclic design construction methods and examples along with additional results of the experiment are provided at http://www.jax.org/staff/churchill/labsite/pubs/yong.
authors.affiliation: The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA.
authors.forename: Yong
authors.initials: Y
authors.lastname: Woo
authors.forename: Winfried
authors.initials: W
authors.lastname: Krueger
authors.forename: Anupinder
authors.initials: A
authors.lastname: Kaur
authors.forename: Gary
authors.initials: G
authors.lastname: Churchill
mesh_terms: D000465:Algorithms; D000818:Animals; D003116:Color; D019295:Computational Biology / Q000379:methods*; D003627:Data Interpretation, Statistical; D020224:Expressed Sequence Tags; D051379:Mice; D008810:Mice, Inbred C57BL; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software