Correction of Spatial Bias in Oligonucleotide Array Data
Joint Authors
Lemieux, Sébastien
Serhal, Philippe
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-03-13
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Natural & Life Sciences (Multidisciplinary)
Biology
Abstract EN
Background.
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’s 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.
Results.
We propose an algorithm, pyn, 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.
Conclusions.
The proposed algorithm increases both precision and accuracy, while requiring virtually no changes to users’ 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.
American Psychological Association (APA)
Serhal, Philippe& Lemieux, Sébastien. 2013. Correction of Spatial Bias in Oligonucleotide Array Data. Advances in Bioinformatics،Vol. 2013, no. 2013, pp.1-9.
https://search.emarefa.net/detail/BIM-451262
Modern Language Association (MLA)
Serhal, Philippe& Lemieux, Sébastien. Correction of Spatial Bias in Oligonucleotide Array Data. Advances in Bioinformatics No. 2013 (2013), pp.1-9.
https://search.emarefa.net/detail/BIM-451262
American Medical Association (AMA)
Serhal, Philippe& Lemieux, Sébastien. Correction of Spatial Bias in Oligonucleotide Array Data. Advances in Bioinformatics. 2013. Vol. 2013, no. 2013, pp.1-9.
https://search.emarefa.net/detail/BIM-451262
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-451262