minfi (version 1.18.2)

preprocessNoob: The Noob background correction for 450k arrays.

Description

Noob is a background correction method with dye-bias normalization for the Illumina Infinium HumanMethylation450 platform.

Usage

preprocessNoob(rgSet, offset = 15, dyeCorr = TRUE, verbose = TRUE)

Arguments

rgSet

An object of class RGChannelSet.

offset

An offset for the normexp background correction.

dyeCorr

Should dye correction be done?

verbose

Should the function be verbose?

Value

• An object of class MethylSet.

References

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:http://www.dx.doi.org/10.1093/nar/gkt090{10.1093/nar/gkt090}.

See Also

RGChannelSet as well as IlluminaMethylationManifest for the basic classes involved in these functions. preprocessRaw and preprocessQuantile are other preprocessing functions.

Examples

if (require(minfiData)) {
  GRset.noob <- preprocessNoob(RGsetEx)
}