preprocessNoob {minfi} | R Documentation

## 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)

[Package minfi version 1.36.0 Index]