Multifactorial experimental design and the transitivity of ratios with spotted DNA microarrays

BMC Genomics. 2003 Oct 2;4(1):41. doi: 10.1186/1471-2164-4-41.


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.

Publication types

  • Evaluation Study

MeSH terms

  • Gene Expression Profiling / methods*
  • Oligonucleotide Array Sequence Analysis / methods*
  • Open Reading Frames
  • RNA, Messenger / analysis
  • Reproducibility of Results
  • Research Design


  • RNA, Messenger