%0 Journal Article %1 Triche:2013:Nucleic-Acids-Res:23476028 %A Triche, T J %A Weisenberger, D J %A Van Den Berg, D %A Laird, P W %A Siegmund, K D %D 2013 %J Nucleic Acids Res %K MUSTREAD epic fulltext illumina methylation microarray minfi quality-control software %N 7 %R 10.1093/nar/gkt090 %T Low-level processing of Illumina Infinium DNA Methylation BeadArrays %U https://www.ncbi.nlm.nih.gov/pubmed/23476028 %V 41 %X We propose a novel approach to background correction for Infinium HumanMethylation data to account for technical variation in background fluorescence signal. Our approach capitalizes on a new use for the Infinium I design bead types to measure non-specific fluorescence in the colour channel opposite of their design (Cy3/Cy5). This provides tens of thousands of features for measuring background instead of the much smaller number of negative control probes on the platforms (n = 32 for HumanMethylation27 and n = 614 for HumanMethylation450, respectively). We compare the performance of our methods with existing approaches, using technical replicates of both mixture samples and biological samples, and demonstrate that within- and between-platform artefacts can be substantially reduced, with concomitant improvement in sensitivity, by the proposed methods.

@article{Triche:2013:Nucleic-Acids-Res:23476028, abstract = {We propose a novel approach to background correction for Infinium HumanMethylation data to account for technical variation in background fluorescence signal. Our approach capitalizes on a new use for the Infinium I design bead types to measure non-specific fluorescence in the colour channel opposite of their design (Cy3/Cy5). This provides tens of thousands of features for measuring background instead of the much smaller number of negative control probes on the platforms (n = 32 for HumanMethylation27 and n = 614 for HumanMethylation450, respectively). We compare the performance of our methods with existing approaches, using technical replicates of both mixture samples and biological samples, and demonstrate that within- and between-platform artefacts can be substantially reduced, with concomitant improvement in sensitivity, by the proposed methods.}, added-at = {2018-07-22T16:22:21.000+0200}, author = {Triche, T J and Weisenberger, D J and Van Den Berg, D and Laird, P W and Siegmund, K D}, biburl = {https://www.bibsonomy.org/bibtex/2568ce2cec5f3c6d6c3953180002558ac/marcsaric}, description = {Low-level processing of Illumina Infinium DNA Methylation BeadArrays. - PubMed - NCBI}, doi = {10.1093/nar/gkt090}, interhash = {5708f10a9fb1d84f8239f5e61b27daba}, intrahash = {568ce2cec5f3c6d6c3953180002558ac}, journal = {Nucleic Acids Res}, keywords = {MUSTREAD epic fulltext illumina methylation microarray minfi quality-control software}, month = apr, number = 7, pmid = {23476028}, timestamp = {2018-07-22T16:22:21.000+0200}, title = {Low-level processing of Illumina Infinium DNA Methylation BeadArrays}, url = {https://www.ncbi.nlm.nih.gov/pubmed/23476028}, volume = 41, year = 2013 }