normalizeBetweenAlleles.SNP: between Allele normalization

In beadarraySNP: Normalization and reporting of Illumina SNP bead arrays

Description

Perform between Allele normalization on Illumina Golden Gate bead arrays

Usage

   normalizeBetweenAlleles.SNP(object,method=c("quantile"),subsample="OPA")

Arguments

object	class SnpSetIllumina
method	char, type of normalization
subsample	factor with length number of features in object or char,column name in featureData slot

Details

This function performs a quantile normalization between the Red and Green channels for each sample. The rationale for this procedure stems from the fact that the allele frequencies within each channel are always very similar, even in the presence of genomic abnormalities.

Value

This function returns an SnpSetIllumina object.

Author(s)

Jan Oosting

See Also

SnpSetIllumina-class,normalizeWithinArrays.SNP, backgroundCorrect.SNP

Examples

data(chr17.260)
data.nrm<-normalizeBetweenAlleles.SNP(chr17.260)

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