backgroundCorrect.SNP: Background correction

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

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")

beadarraySNP documentation built on Nov. 8, 2020, 7:21 p.m.