Cross reactive probes

[mitchwjnorris]

exclude cross reactive probes

xReactiveProbes <- read.csv(file=paste(dataDirectory,
"48639-non-specific-probes-Illumina450k.csv",
sep="/"), stringsAsFactors=FALSE)
keep <- !(featureNames(mSetSqFlt) %in% xReactiveProbes$TargetID)
table(keep)

Chen, Yi-an, Mathieu Lemire, Sanaa Choufani, Darci T Butcher, Daria Grafodatskaya, Brent W Zanke, Steven Gallinger, Thomas J Hudson, and Rosanna Weksberg. 2013. “Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray.” Epigenetics : Official Journal of the DNA Methylation Society 8 (2). Landes Bioscience:203–9. https://doi.org/10.4161/epi.23470.