2013
DOI: 10.4161/epi.27119
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A systematic assessment of normalization approaches for the Infinium 450K methylation platform

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Cited by 64 publications
(58 citation statements)
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“…These results are similar to those reported by other researchers. [12][13][14] However, for SQN, although the bias is reduced, the correlation/difference between the WGBS and its normalized 450K data, and that between technical replicates, is severely compromised, which was already shown in the above analyses. Hence, PBC and QN.…”
Section: 13mentioning
confidence: 54%
See 1 more Smart Citation
“…These results are similar to those reported by other researchers. [12][13][14] However, for SQN, although the bias is reduced, the correlation/difference between the WGBS and its normalized 450K data, and that between technical replicates, is severely compromised, which was already shown in the above analyses. Hence, PBC and QN.…”
Section: 13mentioning
confidence: 54%
“…To address this issue, several comparisons of different preprocessing approaches have been conducted, [12][13][14] mostly assessing reproducibility of technical replicates, reduction of probe design bias and the influence of downstream differential methylation analysis. As a result, BMIQ was the most recommended method, and Marabita et al even preferred a QN plus BMIQ (QN.BMIQ) analysis pipeline, which first quantile-normalized the intensities of methylation signals among all arrays and then used BMIQ to normalize the b-values within each array.…”
mentioning
confidence: 99%
“…There is consensus that Infinium 450K β-values should be normalized (28, 29) and several methods have been proposed. We considered three normalization methods (minfi-Illumina, SWAN and DASEN) in addition to using raw (un-normalized) β-values.…”
Section: Resultsmentioning
confidence: 99%
“…In addition to the BMIQ performed for this analysis, we evaluated various normalization methods in this dataset and observed little impact on the results (31). …”
Section: Discussionmentioning
confidence: 99%