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)

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