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. © 2008 Potter et al; licensee BioMed Central Ltd.
Potter, D. P., Yan, P., Huang, T. H. M., & Lin, S. (2008). Probe signal correction for differential methylation hybridization experiments. BMC Bioinformatics, 9. https://doi.org/10.1186/1471-2105-9-453