Berlin 2008 – scientific programme
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BP: Fachverband Biologische Physik
BP 7: Posters I
BP 7.9: Poster
Monday, February 25, 2008, 17:00–19:30, Poster A
Modeling Background Intensity in Affymetrix GeneChips — •K. Myriam Kroll1, Gerard Barkema2,3, and Enrico Carlon1 — 1Institute of Theoretical Physics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium — 2Institute for Theoretical Physics, Universiteit Utrecht, Leuvenlaan 4, 3584 CE, Utrecht, The Netherlands — 3Institute-Lorentz for Theoretical Physics, University of Leiden, Niels Bohrweg 2, 2333 CA Leiden, The Netherlands
A new physical model for the calculation of the background intensity in Affymetrix GeneChips is introduced. We identify two major sources of background noise; the first is related to the sequence composition (CG-rich sequences are expected to have higher affinities for non-specific hybridization than e.g. AT-rich sequences). The second is due to local dependence of intensities from locations which are the physical neighbors of a specific spot on the chip. Both effects are incorporated in a background functional whose free parameters are fixed via minimization on a training data set. In all data analyzed, the sequence specific parameters strongly correlate with empirically determined stacking free energies in solution. Moreover, we find an overall agreement with experimental background data. We show that our physics/physical-chemistry model globally performs better in calculating background intensities than approaches which are only based upon statistics. Thus, our model provides an interesting alternative method for background subtraction schemes in Affymetrix GeneChips.