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Open Access Research article

Probe signal correction for differential methylation hybridization experiments

Dustin P Potter13*, Pearlly Yan12, Tim HM Huang12 and Shili Lin34*

Author Affiliations

1 Human Cancer Genetics Program, OSU Comprehensive Cancer Center, The Ohio State University, Columbus, OH USA

2 Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, 460 W. 12th Avenue, Columbus, OH USA

3 Mathematical Biosciences Institute, The Ohio State University, 231 W. 18th Avenue, Columbus, OH USA

4 Department of Statistics, The Ohio State University, 1598 Neil Avenue, Columbus, OH USA

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BMC Bioinformatics 2008, 9:453  doi:10.1186/1471-2105-9-453

Published: 23 October 2008

Abstract

Background

Non-biological signal (or noise) has been the bane of microarray analysis. Hybridization effects related to probe-sequence composition and DNA dye-probe interactions have been observed in differential methylation hybridization (DMH) microarray experiments as well as other effects inherent to the DMH protocol.

Results

We suggest two models to correct for non-biologically relevant probe signal with an overarching focus on probe-sequence composition. The estimated effects are evaluated and the strengths of the models are considered in the context of DMH analyses.

Conclusion

The majority of estimated parameters were statistically significant in all considered models. Model selection for signal correction is based on interpretation of the estimated values and their biological significance.