Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 100, Issue 13, Pages 7575-7580Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.0832500100
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A method of analyzing DNA microarray data based on the physical modeling of hybridization is presented. We demonstrate, in experimental data, a correlation between observed hybridization intensity and calculated free energy of hybridization. Then, combining hybridization rate equations, calculated free energies of hybridization, and microarray data for known target concentrations, we construct an algorithm to compute transcript concentration levels from microarray data. We also develop a method for eliminating outlying data points identified by our algorithm. We test the efficacy of these methods by comparing our results with an existing statistical algorithm, as well as by performing a cross-validation test on our model.
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