title: Linear model for fast background subtraction in oligonucleotide microarrays.
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 extended nearest-neighbor model.
  
  
  CONCLUSIONS
  The algorithm has been tested on 360 GeneChips from publicly available data of recent expression experiments. The algorithm is fast and accurate. Strong correlations between the fitted values for different experiments as well as between the free-energy parameters and their counterparts in aqueous solution indicate that the model captures a significant part of the underlying physical chemistry.
authors.affiliation: Institute for Theoretical Physics, Katholieke Universiteit Leuven, Celestijnenlaan 200D, Leuven, Belgium. myriam.kroll@fys.kuleuven.be
authors.forename: K Myriam
authors.initials: KM
authors.lastname: Kroll
authors.forename: Gerard T
authors.initials: GT
authors.lastname: Barkema
authors.forename: Enrico
authors.initials: E
authors.lastname: Carlon