Infinium humanmethylation27 arrays

The same DNA mixes used in the MeDIP experiments were also processed with Illumina’s Infinium HumanMethylation27 arrays. The bisulfite conversion of DNA was done using Zymo Gold kit; the Illumina array processing was performed according to standard protocols. Each sample was done in duplicate.
Raw data (beta values) was extracted from Illumina Bead Studio (version V2011.1). Methylation data was further processed via the Bioconductor lumi package [51 (link)], which works on M values rather than on beta values. The relationship between beta and M values is given as [52 (link)]: $M={log}_2\frac{\beta }{1-\beta }$
We used shift-scale color bias adjustment and quantile normalization as further preprocessing steps implemented in the lumi package. A detection p value cutoff of 0.00001 was used to filter out signals below background, and only CpGs in autosomes were considered. We used limma [53 ] to assess differential methylation of CpG sites between patient groups. Cross reactive loci were defined as described by Chen Y et al, [54 (link)]

The promoter methylation data we used is based on Illumina Infinium HumanMethylation27 arrays to profile DNA methylation at gene promoters of TCGA [13 (link)], targeting 27,578 CpG sites located in proximity to the transcription start sites of 14,475 consensus coding sequencing (CCDS) in the NCBI Database (Genome Build 36). We computed for each gene the methylation level in those genomes where the gene has a repeat instability in its promoter, and compared it to the gene’s methylation level in genomes where the gene has no repeat instability.