normalizeScale {limma}R Documentation

Normalize Columns of a Matrix to have the Same Scale

Description

Performs scale normalization of an M-value matrix or an A-value matrix across a series of arrays. Users do not normally need to call these functions directly - use normalizeBetweenArrays instead.

Usage

normalizeMedianDeviations(x)
normalizeMedians(x)

Arguments

x numeric matrix

Details

If x is a matrix of log-ratios of expression (M-values) then normalizeMedianDeviations is very similar to scaling to equalize the median absolute deviation (MAD) as in Yang et al (2001, 2002). Here the median-absolute value is used for preference to as to not re-center the M-values.

normalizeMedians is used for A-values of overall expression.

Value

normalizeMedianDeviations produces a numeric matrix of the same size as that input which has been scaled so that each column as the same median-absolute value.
normalizeMedians produces a numeric matrix which has been scaled so that each column has the same median-value.

Author(s)

Gordon Smyth

See Also

An overview of LIMMA functions for normalization is given in 4.Normalization.

Examples

M <- cbind(Array1=rnorm(10),Array2=2*rnorm(10))
normalizeMedianDeviations(M)

A <- cbind(Array1=rlnorm(10),Array2=2*rlnorm(10))
normalizeMedians(A)

[Package limma version 1.6.7 Index]