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Updated: Aug 11, 2026

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
Published on: November 3, 2010
Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays
1Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, CA 94720, USA. townsend@nature.berkeley.edu
Background:
Multifactorial experimental designs using DNA microarrays are becoming increasingly common, but the extent of the transitivity of cDNA microarray expression measurements across multiple samples has yet to be explored.
Results:
A strong correlation between direct and transitive inference for significantly differentially expressed genes is demonstrated, using subsets of a dye-swap loop design.
Conclusions:
In experimental design, opportunities for transitive inference should be exploited, while always ensuring that comparisons of greatest interest comprise direct hybridizations.
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