backgroundNormalise {beadarray} | R Documentation

## Background Normalisation for Bead Summary Data objects

### Description

Normalise expression matrix using values of negative controls

### Usage

    backgroundNormalise(object)

### Arguments

`object` | An ExpressionSetIllumina object

### Details

This function implements the background normalisation method recommened by Illumina. All normalisation options in BeadStudio (with the exception of no normalisation) include background normalisation as a first step.

The QC object contains averaged values for the Illumina negative controls placed on each array in an experiment. For background normalisation, we simply subtract the value of the negative control on a particular array from all bead summary values on that array.

Note that this background normalisation is in addition to a local background correction performed at the bead level and is liable to create negative values for genes with low expression. It is therefore not advisable if you wish to analyse data on a log2 scale.

### Value

Expression matrix containing normalise values with the same dimensions as the input

### Author(s)

Mark Dunning

### Examples

    #data(BSData)

    #BSData.bgnorm = backgroundNormalise(BSData)

[Package beadarray version 1.4.0 Index]