ChemoSpec (version 4.3.34)

normSpectra: 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. "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 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.

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.

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)