title: Global assessment of cross-hybridization for oligonucleotide arrays.
abstract: 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 MAS 5.0 difficult.
authors.affiliation: Division of Biostatistics, University of Minnesota, A448 Mayo Bldg., MMC 303, 420 Delaware St. SE, Minneapolis, MN 55455-0378, USA. cavanr@biostat.umn.edu
authors.forename: Cavan
authors.initials: C
authors.lastname: Reilly
authors.forename: Arvind
authors.initials: A
authors.lastname: Raghavan
authors.forename: Paul
authors.initials: P
authors.lastname: Bohjanen
mesh_terms: D018106:CD28 Antigens / Q000737:chemistry; D017252:CD3 Complex / Q000737:chemistry; D019295:Computational Biology; D003627:Data Interpretation, Statistical; D005786:Gene Expression Regulation; D023281:Genomics / Q000379:methods*; D006801:Humans; D008214:Lymphocytes / Q000378:metabolism; D015233:Models, Statistical; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D012984:Software
chemical_list: D018106:CD28 Antigens; D017252:CD3 Complex; D015345:Oligonucleotide Probes