Global assessment of cross-hybridization for oligonucleotide arrays

Cavan Reilly, Arvind Raghavan, Paul Bohjanen

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Cross-hybridization is the tendency for chains of nucleic acids to bind to other chains of nucleic acids that have similar but not identical sequences. This has the potential to make the interpretation of microarray experiments difficult since intensity at a spot on the array does not simply depend on the quantity of target in the sample. We propose a method for evaluating the extent of cross-hybridization in oligonucleotide arrays for data arising from a typical microarray experiment. We show that the level of cross-hybridization can be quite substantial. We argue that this makes the interpretation of the difference calls provided by MAS5.0 difficult.

Original languageEnglish (US)
Pages (from-to)163-172
Number of pages10
JournalJournal of Biomolecular Techniques
Issue number2
StatePublished - Apr 2006


  • Cross-hybridization
  • Detection calls
  • Oligonucleotide arrays


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