beadarraySNP (version 1.38.0)

normalizeBetweenSubsamples.SNP: Normalization between subsamples

Description

Quantile normalization between subsamples within a single SnpSetIllumina object

Usage

normalizeBetweenSubsamples.SNP(object, subsample = "OPA")

Arguments

object

class SnpSetIllumina

subsample

factor with length number of features in object or char,column name in featureData slot

Value

This function returns an SnpSetIllumina object.

Details

Perform quantile normalization of the red and green channel between subsamples. This can be used in situations where multiple different assays that cover the same genomic regions (or whole genome) have been done on the same biological specimen. This function was introduced for version 5 Golden Gate Linkage analysis that consist of 4 assays of ~ 1500 probes. Where previous versions of this assay each targeted a number of chromosomes, in version 5 each assay covers the whole genome.

See Also

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

Examples

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