Abstract
We introduce a computational method which estimates non-specific binding associated with hybridization signal intensities on the oligonucleotide-based Affymetrix GeneChip arrays. We consider a simplified linear hybridization model that should work well when the target DNA concentration is low or when the probe-target affinity is weak, and use the quadratic programming technique to estimate the parameters of this model (binding coefficients). We show that binding coefficients correlate with the degree of homology between the probe and target sequences. Detectable contribution into DNA binding was found to start from the matches of 7–8 nucleotides. The method suggested here may prove useful for the interpretation of hybridization results and for the assessment of true target concentrations in microarray experiments.
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Kachalo, S., Arbieva, Z., Liang, J. (2004). Assessing the Potential Effect of Cross-Hybridization on Oligonucleotide Microarrays. In: Johnson, K.F., Lin, S.M. (eds) Methods of Microarray Data Analysis III. Springer, Boston, MA. https://doi.org/10.1007/0-306-48354-8_13
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DOI: https://doi.org/10.1007/0-306-48354-8_13
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4020-7582-7
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