DNA methylation levels are highly correlated between pooled samples and averaged values when analysed using the Infinium HumanMethylation450 BeadChip array

Table 2 R packages and instructions. Specific instructions used from each R package

R package	Instruction	Description
methylumi	methylumiR	Load Illumina methylation data into a MethyLumiSet object.
minfi	densityPlot	Density plots of methylation Beta values.
watRmelon	pfilter	Filter data sets based on bead count and detection p-values
minfi	mdsPlot	Multi-dimensional scaling (MDS) plots showing a 2-d projection of distances between samples.
watRmelon	dasen	Calculate normalized betas from Illumina 450 K methylation arrays.
lumi	estimateBetas	Estimate methylation Beta-value matrix from eSet-class object (include methylated and unmethylated probe intensities)

ISSN: 1868-7083