Department 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.