Optimal designs for one- and two-color microarrays using mixed models: a comparative evaluation of their efficiencies

• Published in: Journal of computational biology Vol. 16; no. 1; p. 67
• Main Authors: Lima Passos, Valéria, Tan, Frans E S, Winkens, Bjorn, Berger, Martijn P F
• Format: Journal Article
• Language: English
• Published: United States 01.01.2009
• Subjects: Color; Computational Biology - methods; Efficiency; Gene Expression Profiling - economics; Gene Expression Profiling - methods; Oligonucleotide Array Sequence Analysis - economics; Oligonucleotide Array Sequence Analysis - methods
• DOI: 10.1089/cmb.2008.0048

Comparative studies between the one- and two-color microarrays provide supportive evidence for similarities of results on differential gene expression. So far, no design comparisons between the two platforms have been undertaken. With the objective of comparing optimal designs of one- and two-color microarrays in their statistical efficiencies, techniques of design optimization were applied within a mixed model framework. A- and D-optimal designs for the one- and two-color platforms were sought for a 3 x 3 factorial experiment. The results suggest that the choice of the platform will not affect the "subjects to groups" allocation, being concordant in the two designs. However, under financial constraints, the two-color arrays are expected to have a slight upper hand in terms of efficiency of model parameters estimates, once the price of arrays is more expensive than that of subjects. This statement is especially valid for microarray studies envisaging class comparisons.