beadarraySNP (version 1.38.0)

normalizeBetweenAlleles.SNP: between Allele normalization

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

Value

This function returns an SnpSetIllumina object.

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.

See Also

SnpSetIllumina-class,normalizeWithinArrays.SNP, backgroundCorrect.SNP

Examples

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