rankIvariantNormalise {beadarray}R Documentation

Rank Invariant normalise data in a matrix

Description

Normalise expression matrix using rank invariant genes

Usage

rankInvariantNormalise(exprs, T)

Arguments

exprs a matrix of expression values
T A target distribution vector to normalise the data to. The default is NULL in which case the average quantiles are used

Details

Using the normalize.invariantset function from the affy package, we find a list of rank invariant genes whose rank does not change significantly between the columns of exprs. We then fit a normalising curve to each array using the values of the rank invariant genes of the array and a target distribution.

The target distribution may be specified by the user and by default is the vector of average quantiles across all arrays.

Value

Matrix of normalised expression data with the same dimensions as exprs.

Author(s)

Mark Dunning

Examples

data(BSData)

BSData.ri  = assayDataElementReplace(BSData, "exprs", rankInvariantNormalise(exprs(BSData)))

[Package beadarray version 1.10.0 Index]