normalize: Quantitative data normalisation

In rformassspectrometry/MsCoreUtils: Core Utils for Mass Spectrometry Data

Quantitative data normalisation

Description

Function to normalise a matrix of quantitative omics data. The nature of the normalisation is controlled by the method argument, described below.

Usage

normalizeMethods()

normalize_matrix(x, method, ...)

Arguments

x	A matrix or an HDF5Matrix object to be normalised.
method	character(1) defining the normalisation method. See normalizeMethods() for available ones.
...	Additional parameters passed to the inner normalisation function.

Details

The method parameter can be one of "sum", "max", "center.mean", "center.median", "div.mean", "div.median", "diff.median", ⁠"quantiles⁠", ⁠"quantiles.robust⁠" or "vsn". The normalizeMethods() function returns a vector of available normalisation methods.

• For "sum" and "max", each feature's intensity is divided by the maximum or the sum of the feature respectively. These two methods are applied along the features (rows).

• "center.mean" and "center.median" center the respective sample (column) intensities by subtracting the respective column means or medians. "div.mean" and "div.median" divide by the column means or medians.

• "diff.median" centers all samples (columns) so that they all match the grand median by subtracting the respective columns medians differences to the grand median.

• Using "quantiles" or "quantiles.robust" applies (robust) quantile normalisation, as implemented in preprocessCore::normalize.quantiles() and preprocessCore::normalize.quantiles.robust(). "vsn" uses the vsn::vsn2() function. Note that the latter also glog-transforms the intensities. See respective manuals for more details and function arguments.

Value

A matrix of same class as x with dimensions dim(x).

Author(s)

Laurent Gatto

See Also

The scale() function that centers (like center.mean above) and scales.

Examples

normalizeMethods()

## test data
set.seed(42)
m <- matrix(rlnorm(60), 10)

normalize_matrix(m, method = "sum")

normalize_matrix(m, method = "max")

normalize_matrix(m, method = "quantiles")

normalize_matrix(m, method = "center.mean")

rformassspectrometry/MsCoreUtils documentation built on Oct. 24, 2024, 1:52 p.m.