Normalize Columns of a Matrix to have the Median Absolute Value
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.
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.
M <- cbind(Array1=rnorm(10),Array2=2*rnorm(10)) normalizeMedianAbsValues(M)
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