rankIvariantNormalise {beadarray}R Documentation

Rank Invariant Normalisation for Bead Summary data

Description

Normalise expression matrix using rank invariant genes

Usage

rankInvariantNormalise(exprs, T)

Arguments

exprs An expression matrix from a ExpressionSet object
T A target distribution vector used to normalise to. The default is NULL in which case the average quantiles are used

Details

Using the normalize.invariantset from affy, 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

Expression matrix with the same dimensions as the input

Author(s)

Mark Dunning

Examples


data(BSData)

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



[Package beadarray version 1.2.2 Index]