preprocessNoob: The Noob/ssNoob preprocessing method for Infinium methylation...

In hansenlab/minfi: Analyze Illumina Infinium DNA methylation arrays

The Noob/ssNoob preprocessing method for Infinium methylation microarrays.

Description

Noob (normal-exponential out-of-band) is a background correction method with dye-bias normalization for Illumina Infinium methylation arrays.

Usage

preprocessNoob(rgSet, offset = 15, dyeCorr = TRUE, verbose = FALSE,
               dyeMethod=c("single", "reference"))

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?
dyeMethod	How should dye bias correction be done: use a single sample approach (ssNoob), or a reference array?

Value

An object of class MethylSet.

Author(s)

Tim Triche, Jr.

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: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)) {
  ## 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)

hansenlab/minfi documentation built on May 3, 2024, 3:49 p.m.