cnrma {crlmm}R Documentation

Quantile normalizes the intensities for the nonpolymorphic probe to a HapMap reference distribution.

Description

Quantile normalizes the intensities for the nonpolymorphic probe to a HapMap reference distribution.

Usage

cnrma(filenames, cdfName="genomewidesnp6", sns, seed = 1, verbose=FALSE)

Arguments

filenames filenames with complete path
cdfName Only 'genomewidesnp6' allowed
sns the sample names. If missing, the basename of the filenames is used.
seed seed for sampling the intensities to calculate skewness
verbose logical

Value

A list. First element is the matrix of quantile-normalized intensities. The second element is the skew.

Note

Not tested

Author(s)

Rob Scharpf

Examples

        library(genomewidesnp6Crlmm)
        library(hapmapsnp6)
        path <- system.file("celFiles", package="hapmapsnp6")
        celFiles <- list.celfiles(path, full.names=TRUE)
        cnrmaResult <- cnrma(celFiles, cdfName="genomewidesnp6")

[Package crlmm version 1.2.4 Index]