CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments.
BACKGROUND
DNA microarrays contain thousands of different probe sequences represented on their surface. These are designed in such a way that potential cross-hybridization reactions with non-target sequences are minimized. However, given the large number of probes, the occurrence of cross hybridization events cannot be excluded. This problem can dramatically affect the data quality and cause false positive/false negative results.


RESULTS
CrossHybDetector is a software package aimed at the identification of cross-hybridization events occurred during individual array hybridization, by using the probe sequences and the array intensity values. As output, the software provides the user with a list of array spots potentially 'corrupted' and their associated p-values calculated by Monte Carlo simulations. Graphical plots are also generated, which provide a visual and global overview of the quality of the microarray experiment with respect to cross-hybridization issues.


CONCLUSIONS
CrossHybDetector is implemented as a package for the statistical computing environment R and is freely available under the LGPL license within the CRAN project.
Uva
Paolo
P
Istituto di Ricerche di Biologia Molecolare, Merck Research Laboratories, Rome, Italy. paolo_uva@merck.com
de Rinaldis
Emanuele
E
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D015342:DNA Probes; D030541:Databases, Genetic; D009010:Monte Carlo Method; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012984:Software
D015342:DNA Probes