Probe signal correction for differential methylation hybridization experiments

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. Background With the advent of microarray technology, whole genome DNA methylation profiling has become a common approach to understand the systemic effects of this aberrant epigenomic mark ...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Dustin P. Potter, Pearlly Yan, Tim Hui-Ming Huang, Shili Lin
• Keywords: BMCBI 2008, DNA Methylation, Genome Dna Methylation, Probe-sequence Composition