normaliseIllumina {beadarray}R Documentation

Normalise Illumina expression data

Description

Normalises expression intensities so that the intensities are comparable between arrays.

Usage

normaliseIllumina(BSData, method="quantile", transform="none", T=NULL)

Arguments

BSData an 'ExpressionSetIllumina' object
method character string specifying normalisation method (options are "quantile", "qspline", "vsn", "rankInvariant", "median" and "none".
transform character string specifying transformation to apply to the data (options are "none", "log2" and "vst"
T A target distribution vector used in "rankInvariant" normalisation. If NULL, the mean is used.

Details

Normalisation is intended to remove from the expression measures any systematic trends which arise from the microarray technology rather than from differences between the probes or between the target RNA samples hybridized to the arrays.

When transform="vst" the variance stabilising transformation from the 'lumi' package is applied to the data. Refer to the 'lumi' documentation for further particulars.

For further particulars on the different normalisation methods options refer to the individual help pages (?normalize.quantiles for "quantile", ?normalize.qspline for "qspline", ?rankInvariantNormalise for "rankInvariant", ?medianNormalise for "median" and ?vsn2 for "vsn".

For median normalisation, the intensity for each gene is adjusted by subtracting the median of all genes on the array and then adding the median across all arrays. The effect is that each array then has the same median value.

Note: If your BSData object contains data already on the log-scale, be careful that you choose an appropriate transform to avoid logging it twice. The same applies for the "vst" transformation and "vsn" normalisation methods which require the expression data stored in BSData to be on the original (un-logged) scale.

Value

An 'ExpressionSetIllumina' object which conatains the transformed and normalised expression values for each array.

Author(s)

Matt Ritchie

Examples

data(BSData)
BSData.norm = normaliseIllumina(BSData, method="quantile", transform="log2")

[Package beadarray version 1.6.0 Index]