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Bioinformatics. 2005 Jun;21 Suppl 1:i459-67.

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

Author information

1
The Jackson Laboratory 600 Main Street, Bar Harbor, ME 04609, USA.

Abstract

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

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.

PMID:
15961491
DOI:
10.1093/bioinformatics/bti1031
[Indexed for MEDLINE]

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