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

Description Usage Arguments Details Value Author(s) See Also Examples

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

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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

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

richierocks/limma2 documentation built on May 27, 2019, 8:47 a.m.