title: Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays.
abstract: 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.
authors.affiliation: Department of Plant and Microbial Biology, 321 Koshland Hall, University of California, Berkeley, CA 94720, USA. townsend@nature.berkeley.edu
authors.forename: Jeffrey P
authors.initials: JP
authors.lastname: Townsend
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D016366:Open Reading Frames; D012333:RNA, Messenger / Q000032:analysis; D015203:Reproducibility of Results; D012107:Research Design
chemical_list: D012333:RNA, Messenger