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Báo cáo sinh học: "Linear model for fast background subtraction in oligonucleotide microarrays"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Linear model for fast background subtraction in oligonucleotide microarrays. | Algorithms for Molecular Biology BioMed Central Open Access Software article Linear model for fast background subtraction in oligonucleotide microarrays K Myriam Kroll1 Gerard T Barkema2 3 and Enrico Carlon 1 Address institute for Theoretical Physics Katholieke Universiteit Leuven Celestijnenlaan 200D Leuven Belgium institute for Theoretical Physics Utrecht University Leuvenlaan 4 3584 CE Utrecht the Netherlands and 3Instituut-Lorentz for Theoretical Physics University of Leiden Niels Bohrweg 2 2333 CA Leiden the Netherlands Email K Myriam Kroll - myriam.kroll@fys.kuleuven.be Gerard T Barkema - G.T.Barkema@phys.uu.nl Enrico Carlon - enrico.carlon@fys.kuleuven.be Corresponding author Published 16 November 2009 Received 21 July 2009 r J. 1 I mz i-rzn-rmn z ir Accepted 16 November 2009 Algorithms for Molecular Biology 2009 4 15 doi 10.1186 1748-7188-4-15 This article is available from http www.almob.org content 4 1 15 2009 Kroll et al licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License http creativecommons.org licenses by 2.0 which permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited. Abstract_ Background One important preprocessing step in the analysis of microarray data is background subtraction. In high-density oligonucleotide arrays this is recognized as a crucial step for the global performance of the data analysis from raw intensities to expression values. Results We propose here an algorithm for background estimation based on a model in which the cost function is quadratic in a set of fitting parameters such that minimization can be performed through linear algebra. The model incorporates two effects 1 Correlated intensities between neighboring features in the chip and 2 sequence-dependent affinities for non-specific hybridization fitted by an .