This dataset provides the average methylation values on chromosomes 7 (33-35MG, 105-108MB) of two commercially available EBV transfected lymphoblastoid cell lines from healthy individuals (NA17105 (African American male) and NA17018 (Chinese female), Coriell Institute for Medical Research (NJ, USA)). The dataset also contains the breast cancer cell line MCF7 (Soule et al. 1973) and HPV negative squamous-cell vulva carcinoma cell line A431 (Giard et al. 1973 & Hietanen et al. 1995). Raw data is publically avaliable via the Illumina website and discussed in Bibikova et al. 2009 & 2011. Import and pre-processing was carried out using the LUMI package (Du et al. 2008) in R following the optimized "lumi: QN+BMIQ" pipeline (Marabita et al. 2013). This includes exclusion of poorly performing probes (p<0.01, n=713), color adjustment, quantile normalization and correction for probe type bias (Infinium I vs II) using the BMIQ algorithm (Teschendorf 2013).
This dataset includes the DMRforPairs results of a 4MB region in the CL.methy dataset. This is a small subset of the data used in the vignette to facilitate the examples in the reference manual(104MB-107MB on chr 7). Please see the CL.methy dataset for more details.
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