Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform

PloS One
Claudia SalaChristine Nardini

Abstract

Meta-analysis is a powerful means for leveraging the hundreds of experiments being run worldwide into more statistically powerful analyses. This is also true for the analysis of omic data, including genome-wide DNA methylation. In particular, thousands of DNA methylation profiles generated using the Illumina 450k are stored in the publicly accessible Gene Expression Omnibus (GEO) repository. Often, however, the intensity values produced by the BeadChip (raw data) are not deposited, therefore only pre-processed values -obtained after computational manipulation- are available. Pre-processing is possibly different among studies and may then affect meta-analysis by introducing non-biological sources of variability. To systematically investigate the effect of pre-processing on meta-analysis, we analysed four different collections of DNA methylation samples (datasets), each composed of two subsets, for which raw data from controls (i.e. healthy subjects) and cases (i.e. patients) are available. We pre-processed the data from each dataset with nine among the most common pipelines found in literature. Moreover, we evaluated the performance of regRCPqn, a modification of the RCP algorithm that aims to improve data consistency. For each ...Continue Reading

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Citations

Sep 23, 2021·Genome Biology·Benjamin Planterose JiménezAthina Vidaki

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Datasets Mentioned

BETA
GPL13534
GSE65163
GSE109446
GSE109042

Software Mentioned

BuccalFetalAlcohol
R
minfi
OpenSea
SWAN
wateRmelon
regRCPqn
lme4
devtools
FunNorm

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