The Illumina Infinium HumanMethylation450 BeadChip (450k) is widely used for the evaluation of DNA methylation levels in large-scale datasets, particularly in cancer. The 450k design allows copy number variant (CNV) calling using existing bioinformatics tools. However, in cancer samples, numerous large-scale aberrations cause shifting in the probe intensities and thereby may result in erroneous CNV calling. Therefore, a baseline correction process is needed. We suggest the maximum peak of probe segment density to correct the shift in the intensities in cancer samples.
Availability and implementation: CopyNumber450kCancer is implemented as an R package. The package with examples can be downloaded at http://cran.r-project.org
Contact: nour.marzouka@medsci.uu.se
Supplementary information: Supplementary data are available at Bioinformatics online.
© The Author 2015. Published by Oxford University Press.