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Bioinformatics 2005 21(Suppl 1):i459-i467; doi:10.1093/bioinformatics/bti1031
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

Experimental design for three-color and four-color gene expression microarrays

Yong Woo 1,3, Winfried Krueger 2, Anupinder Kaur 2 and Gary Churchill 1,*

1The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA
2Laboratory for Microarray Technology Department of Genetics and Developmental Biology L40760/4085 University of Connecticut Medical School 263 Farmington Avenue, Farmington, CT 06030, USA
3Functional Genomics PhD Program, The University of Maine Orono, ME 04469, USA

*To whom correspondence should be addressed.

Motivation: 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.

Availability: http://www.jax.org/staff/churchill/labsite/software

Contact: garyc{at}jax.org

Supplementary information: 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

Received on January 15, 2005; accepted on March 27, 2005

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