R: Normalize a Spectra Object

normSpectra {ChemoSpec} | R Documentation

## Normalize a Spectra Object

### Description

This function carries out normalization of the spectra in a `Spectra` object. There are currently four options:

- `"PQN"` carries out "Probabalistic Quotient Normalization" as described in the reference. This is probably the best option for many data sets.

- `"TotInt"` normalizes by total intensity. In this case, the y-data of a `Spectra` object is normalized by dividing each y-value by the sum of the y-values in a given spectrum. Thus each spectrum sums to 1. This method assumes that the total concentration of all substances giving peaks does not vary across samples which may not be true.

- `"Range"` allows one to do something similar but rather than using the sum of the entire spectrum as the denominator, only the sum of the given range is used. This would be appropriate if there was an internal standard in the spectrum which was free of interferance.

- `"zero2one"` scales each spectrum separately to a [0 ... 1] scale. This is sometimes useful for visual comparison of chromatograms but is inappropriate for metabolomic data sets.

### Usage

    normSpectra(spectra, method = "PQN", RangeExpress = NULL)

### Arguments

`spectra` | An object of S3 class `Spectra` to be normalized.
`method` | One of `c("PQN", "TotInt", "Range", "zero2one")` giving the method for normalization.
`RangeExpress` | A logical expression giving the frequency range over which to sum intensities, before dividing the entire spectrum by the summed values. For examples of constructing these expressions, see the examples in `removeFreq`.

### Value

An object of S3 class `Spectra`.

### Author(s)

Bryan A. Hanson, DePauw University.

### References

Probabalistic Quotient Normalization is reported in F. Dieterle et. al. Analytical Chemistry vol. 78 pages 4281-4290 (2006). The exact same mathematics are called "median fold change normalization" by Nicholson's group, reported in K. A. Veselkov et. al. Analytical Chemistry vol. 83 pages 5864-5872 (2011).

https://github.com/bryanhanson/ChemoSpec

### Examples

    data(SrE.IR)
    res <- normSpectra(SrE.IR)
    sumSpectra(res)

[Package ChemoSpec version 4.4.97 Index]