normalise-methods {MSnbase} | R Documentation

## Normalisation of `MSnExp`, `MSnSet` and `Spectrum` objects

### Description

The `normalise` method (also available as `normalize`) performs basic normalisation on spectra intensities of single spectra (`"Spectrum"` or `"Spectrum2"` objects), whole experiments (`"MSnExp"` objects) or quantified expression data (`"MSnSet"` objects).

Raw spectra and experiments are normalised using `max` or `sum` only. For MSMS spectra could be normalised to their `precursor` additionally. Each peak intensity is divided by the highest intensity in the spectrum, the sum of intensities or the intensity of the precursor. These methods aim at facilitating relative peaks heights between different spectra.

The `method` parameter for `"MSnSet"` can be one of `sum`, `max`, `quantiles`, `center.mean`, `center.median`, `.median`, `quantiles.robust` or `vsn`. For `sum` and `max`, each feature's reporter intensity is divided by the maximum or the sum respectively. These two methods are applied along the features (rows).

`center.mean` and `center.median` translate the respective sample (column) intensities according to the column mean or median. `diff.median` translates all samples (columns) so that they all match the grand median. Using `quantiles` or `quantiles.robust` applies (robust) quantile normalisation, as implemented in `normalize.quantiles` and `normalize.quantiles.robust` of the `preprocessCore` package. `vsn` uses the `vsn2` function from the `vsn` package. Note that the latter also glog-transforms the intensities. See respective manuals for more details and function arguments.

A `scale` method, mimicking the base `scale` method exists for `"MSnSet"` instances. See `?base::scale` for details.

### Arguments

`object` | An object of class `"Spectrum"`, `"Spectrum2"`, `"MSnExp"` or `"MSnSet"`.
`method` | A character vector of length one that describes how to normalise the object. See description for details.
`...` | Additional arguments passed to the normalisation function.

### Methods

The `normalise` methods:

`signature(object = "MSnSet", method = "character")`

  Normalises the `object` reporter ions intensities using `method`.

`signature(object = "MSnExp", method = "character")`

  Normalises the `object` peak intensities using `method`.

`signature(object = "Spectrum", method = "character")`

  Normalises the `object` peak intensities using `method`.

`signature(object = "Spectrum2", method = "character", precursorIntensity)`

  Normalises the `object` peak intensities using `method`. If `method == "precursor"`, `precursorIntensity` allows to specify the intensity of the precursor manually.

The `scale` method:

`signature(x = "MSnSet", center = "logical", scale = "logical")`

  See `?base::scale`.

### Examples

    ## quantifying full experiment
    data(msnset)
    msnset.nrm <- normalise(msnset, "quantiles")
    msnset.nrm

[Package MSnbase version 2.12.0 Index]