preprocessNoob {minfi} | R Documentation |
Noob (normal-exponential out-of-band) is a background correction method with dye-bias normalization for Illumina Infinium methylation arrays.
preprocessNoob(rgSet, offset = 15, dyeCorr = TRUE, verbose = FALSE, dyeMethod=c("single", "reference"))
rgSet |
An object of class |
offset |
An offset for the normexp background correction. |
dyeCorr |
Should dye correction be done? |
verbose |
Should the function be verbose? |
dyeMethod |
How should dye bias correction be done: use a single sample approach (ssNoob), or a reference array? |
An object of class MethylSet
.
Tim Triche, Jr.
TJ Triche, DJ Weisenberger, D Van Den Berg, PW Laird and KD Siegmund Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Res (2013) 41, e90. doi:10.1093/nar/gkt090.
RGChannelSet
as well as IlluminaMethylationManifest
for the
basic classes involved in these functions.
preprocessRaw
and preprocessQuantile
are other preprocessing functions.
if (require(minfiData)) { ## RGsetEx.sub is a small subset of RGsetEx; ## only used for computational speed. MsetEx.sub.noob <- preprocessNoob(RGsetEx.sub) } ## Not run: if (require(minfiData)) { dyeMethods <- c(ssNoob="single", refNoob="reference") GRsets <- lapply(dyeMethods, function(m) preprocessNoob(RGsetEx, dyeMethod=m)) all.equal(getBeta(GRsets$refNoob), getBeta(GRsets$ssNoob)) # TRUE } ## End(Not run)