normalizeMedianAbsValues: Normalize Columns of a Matrix to have the Median Absolute...

In hdeberg/limma: Linear Models for Microarray Data

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

normalizeMedianValues(x)
normalizeMedianAbsValues(x)

Arguments

x	numeric matrix

Details

If x is a matrix of log-ratios of expression (M-values) then normalizeMedianAbsValues 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.

normalizeMedianAbsValues is also used to scale the A-values when scale-normalization is applied to an MAList object.

Value

A numeric matrix of the same size as that input which has been scaled so that each column has the same median value (for normalizeMedianValues) or median-absolute value (for normalizeMedianAbsValues).

Author(s)

Gordon Smyth

See Also

An overview of LIMMA functions for normalization is given in 05.Normalization.

Examples

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

hdeberg/limma documentation built on Dec. 20, 2021, 3:43 p.m.