CL.methy: METHYLATION DATA OF 4 CELL LINES (CHR 7)

Description Usage Format Source References

Description

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).

Usage

1

Format

A data frame of 14 variables containing 711 observations. Variables: targetID (probe name), chromosome, position (bp), class.gene.related (functional class related to gene), class.island.related (functional class related to CpG island), gene.symbol, A431.M, MCF7.M, NA17105.M, NA17018.M, A431.beta, MCF7.beta, NA17105.beta, NA17018.beta

Source

Bibikova et al 2009 & 2011, download from Illumina website.

References


DMRforPairs documentation built on May 2, 2018, 4:39 a.m.