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. However, please
be careful if your sample has protein in it, PQN is potentially biased.
See the references.
"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 to
"TotInt" 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, and one wanted to normalize
relative to it.
"zero2one" scales each spectrum separately to a [0 ... 1] scale.
This is sometimes useful for visual comparison of chromatograms but is
inappropriate for spectral data sets.
normSpectra(spectra, method = "PQN", RangeExpress = NULL)
An object of S3 class
Spectra to be normalized.
c("PQN", "TotInt", "Range", "zero2one") giving
the method for normalization.
A vector of
logicals (must be of
length(Spectra$freq)). This vector should be
the frequency range you want to serve as the basis for norming, and
The entire spectrum will be divided by the sum of the
TRUE range. See the examples.
An object of S3 class
Probabalistic Quotient Normalization is reported in F. Dieterle et al. Analytical Chemistry vol. 78 pages 4281-4290 (2006).
The exact same mathematics are called "median fold change normalization" by Nicholson's group, reported in K. A. Veselkov et. al. Analytical Chemistry vol. 83 pages 5864-5872 (2011).
Corriea et al. "1H NMR Signals from Urine Excreted Protein are a Source of Bias in Probablistic Quotient Normalization" Analytical Chemistry vol. 94 pages 6919-6923 (2022).
Additional documentation at https://bryanhanson.github.io/ChemoSpec/
# This example assumes the graphics output is set to ggplot2 (see ?GraphicsOptions). library("ggplot2") data(SrE.IR) # Reference spectrum before normalization p1 <- plotSpectra(SrE.IR) + ggtitle("Original Spectrum") p1 # Default PQN normalization res1 <- normSpectra(SrE.IR) p2 <- plotSpectra(res1) + ggtitle("PQN Normalization") p2 # Norm over carbonyl region RE <- SrE.IR$freq > 1650 & SrE.IR$freq < 1800 res2 <- normSpectra(SrE.IR, method = "Range", RangeExpress = RE) p3 <- plotSpectra(res2) + ggtitle("Normalized to Carbonyl Peaks") p3 # Check numerically rowSums(res2$data[, RE]) # compare to rowSums(SrE.IR$data[,RE]) #>  1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1