backgroundCorrect.SNP {beadarraySNP}R Documentation

Background correction

Description

Perform background correction on Illumina Golden Gate bead arrays

Usage

   backgroundCorrect.SNP(object,method=c("none", "subtract", "half", "minimum",
                         "edwards", "normexp", "rma"),offset = 0)

Arguments

object SnpSetIllumina object
method character, method of correction
offset numeric, constant to add after correction

Details

Code has been ported from the limma package. The matrices Gb and Rb should be available in the arrayData slot of the object.

Value

This function returns an SnpSetIllumina object with background corrected values in the G and R.

Author(s)

Jan Oosting, based on limma package by G. Smyth

See Also

SnpSetIllumina-class, backgroundCorrect, backgroundEstimate, normalizeBetweenAlleles.SNP, normalizeWithinArrays.SNP

Examples

  ## Not run: data.bg<-backgroundCorrect.SNP(data.raw,"subtract")

[Package beadarraySNP version 1.6.0 Index]