Probe signal correction for differential methylation hybridization experiments

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.