beadarraySNP (version 1.38.0)

backgroundCorrect.SNP: 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

Value

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

Details

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

See Also

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

Examples

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