normalizeMedianAbsValues: Normalize Columns of a Matrix to have the Median Absolute...
In limma: Linear Models for Microarray Data

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

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.

1 2	normalizeMedianValues(x) normalizeMedianAbsValues(x)

`x`	numeric matrix

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.

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).

Gordon Smyth

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

1 2	M <- cbind(Array1=rnorm(10),Array2=2*rnorm(10)) normalizeMedianAbsValues(M)

          Array1        Array2
 [1,]  1.2947866  2.0617648997
 [2,] -1.2913844  0.4139565531
 [3,]  0.8523282 -1.5826944996
 [4,]  2.4866680 -1.5439147766
 [5,] -0.4492796 -0.9512867835
 [6,]  1.3500338  1.0422561943
 [7,] -2.0387101 -0.6295432089
 [8,] -0.6538705  2.2463546096
 [9,]  1.4189593 -1.6508832678
[10,] -1.1278923 -0.0009230889