Probe signal correction for differential methylation hybridization experiments

Dustin P. Potter; Pearlly Yan; Tim H.M. Huang; Shili Lin

doi:10.1186/1471-2105-9-453

Probe signal correction for differential methylation hybridization experiments

Dustin P. Potter, Pearlly Yan, Tim H.M. Huang, Shili Lin

Research output: Contribution to journal › Article › peer-review

8 Scopus citations

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.

Original language	English (US)
Article number	453
Journal	BMC bioinformatics
Volume	9
DOIs	https://doi.org/10.1186/1471-2105-9-453
State	Published - Oct 23 2008
Externally published	Yes

ASJC Scopus subject areas

Applied Mathematics
Molecular Biology
Structural Biology
Biochemistry
Computer Science Applications

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10.1186/1471-2105-9-453

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title = "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.",

author = "Potter, {Dustin P.} and Pearlly Yan and Huang, {Tim H.M.} and Shili Lin",

note = "Funding Information: This work is supported by the National Cancer Institute grant U54CA113001. DP is supported in part by the NCI grant T32-CA106196-03. This material is also based upon work partially supported by The National Science Foundation grant DMS-0112050. The authors thank Shuy- ing Sun and Brandilyn Stigler for their valuable discussions. The authors also thank the reviewers for their useful suggestions that helped strengthen the paper.",

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doi = "10.1186/1471-2105-9-453",

language = "English (US)",

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T1 - Probe signal correction for differential methylation hybridization experiments

AU - Potter, Dustin P.

AU - Yan, Pearlly

AU - Huang, Tim H.M.

AU - Lin, Shili

N1 - Funding Information: This work is supported by the National Cancer Institute grant U54CA113001. DP is supported in part by the NCI grant T32-CA106196-03. This material is also based upon work partially supported by The National Science Foundation grant DMS-0112050. The authors thank Shuy- ing Sun and Brandilyn Stigler for their valuable discussions. The authors also thank the reviewers for their useful suggestions that helped strengthen the paper.

PY - 2008/10/23

Y1 - 2008/10/23

N2 - 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.

AB - 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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Probe signal correction for differential methylation hybridization experiments

Abstract

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