Probe signal correction for differential methylation hybridization experiments
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Citation:Dustin P. Potter et al, "Probe signal correction for differential methylation hybridization experiments," BMC Bioinformatics 9 (2008), doi:10.1186/1471-2105-9-453, http://www.biomedcentral.com/1471-2105/9/453
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.
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