A Model Based Background Adjustment for Oligonucleotide Expression Arrays

High density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of further pre-processing and data reduction occurs following the image processing ∗Zhijin Wu is graduate student and Rafael A. Irizarry is Associate Professor of Biostatistics (E-mail: [email protected]), Francisco Martinez Murillo is manager of JHMI Microarray Core, Forrest Spencer is Associate Professor of Medicine and Molecular Biology and Genetics and director of JHMI microarray Core, Johns Hopkins University, Baltimore, Maryland 21205. Robert Gentleman is Associate Professor of Biostatistical Science, Dana–Farber Cancer Institute, 44 Binney Street Boston, MA 02115. The authors would like to thank Terry Speed, Ben Bolstad, and Earl Hubbell for insightful discussions that helped develop our ideas. We would also like to thank Wolfgang Huber and Tom Louis for some helpful comments. The work of Rafael Irizarry is partially funded by the Hopkins PGA (http://www.hopkins-genomics.org) Administrative/Bioinformatics Component (P01 HL 66583). The work of Zhijin Wu is partially funded by the Johnson and Johnson Research Foundation.