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Oligonucleotide microarrays allow for high-throughput gene expression profiling assays. The technology relies on the fundamental assumption that observed hybridization signal intensities (HSIs) for each intended target, on average, correlate with their target\u2019s true concentration in the sample. However, systematic, nonbiological variation from several sources undermines this hypothesis. Background hybridization signal has been previously identified as one such important source, one manifestation of which appears in the form of spatial autocorrelation. <jats:italic>Results<\/jats:italic>. We propose an algorithm, <jats:italic>pyn<\/jats:italic>, for the elimination of spatial autocorrelation in HSIs, exploiting the duality of desirable mutual information shared by probes in a common probe set and undesirable mutual information shared by spatially proximate probes. We show that this correction procedure reduces spatial autocorrelation in HSIs; increases HSI reproducibility across replicate arrays; increases differentially expressed gene detection power; and performs better than  previously published methods. <jats:italic>Conclusions<\/jats:italic>. The proposed algorithm increases both precision and accuracy, while requiring virtually no changes to users\u2019 current analysis pipelines: the correction consists merely of a transformation of raw HSIs (e.g., CEL files for Affymetrix arrays). A free, open-source implementation is provided as an R package, compatible with standard Bioconductor tools. The approach may also be tailored to other platform types and other sources of bias.<\/jats:p>","DOI":"10.1155\/2013\/167915","type":"journal-article","created":{"date-parts":[[2013,4,10]],"date-time":"2013-04-10T08:47:17Z","timestamp":1365583637000},"page":"1-9","source":"Crossref","is-referenced-by-count":2,"title":["Correction of Spatial Bias in Oligonucleotide Array Data"],"prefix":"10.1155","volume":"2013","author":[{"given":"Philippe","family":"Serhal","sequence":"first","affiliation":[{"name":"Institute for Research in Immunology and Cancer (IRIC), Universit\u00e9 de Montr\u00e9al, C.P. 6128, Succursale Centre-Ville, Montr\u00e9al, QC, Canada H3C 3J7"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"S\u00e9bastien","family":"Lemieux","sequence":"additional","affiliation":[{"name":"Institute for Research in Immunology and Cancer (IRIC), Universit\u00e9 de Montr\u00e9al, C.P. 6128, Succursale Centre-Ville, Montr\u00e9al, QC, Canada H3C 3J7"},{"name":"Department of 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