calibrateIntensitymethods  R Documentation 
This function calibrates (normalize) intensities of
MassSpectrum
objects.
## S4 method for signature 'MassSpectrum'
calibrateIntensity(object,
method=c("TIC", "PQN", "median"), range, ...)
## S4 method for signature 'list'
calibrateIntensity(object,
method=c("TIC", "PQN", "median"), range, ...)
object 

method 
the calibration method to be used. This should be one of

range 

... 
arguments to be passed to other functions. Currently only

A number of different calibration methods are provided:
"TIC"
:The TIC (Total Ion Current) of a
MassSpectrum
object is set to one. If range
is
given the TIC is only calculated for the intensities in the
specified mass range.
"PQN"
:The PQN (Probabilistic Quotient
Normalization) is described in Dieterle et al 2006.
calibrateIntensity
uses the following algorithm:
Calibrate all spectra using the "TIC"
calibration.
Calculate a median reference spectrum.
Calculate the quotients of all intensities of the spectra with those of the reference spectrum.
Calculate the median of these quotients for each spectrum.
Divide all intensities of each spectrum by its median of quotients.
"median"
:The median of intensities of a
MassSpectrum
object is set to one.
Returns a modified MassSpectrum
object with calibrated
intensities.
Sebastian Gibb mail@sebastiangibb.de
F. Dieterle, A. Ross, G. Schlotterbeck, and Hans Senn. 2006. Probabilistic quotient normalization as robust method to account for dilution of complex biological mixtures. Application in 1H NMR metabonomics. Analytical Chemistry 78(13): 42814290.
MassSpectrum
Website: https://strimmerlab.github.io/software/maldiquant/
## load package
library("MALDIquant")
## load example data
data("fiedler2009subset", package="MALDIquant")
## baseline correction
b < removeBaseline(fiedler2009subset)
## calibrate intensity values
calibrateIntensity(b, method="TIC")
## calibrate intensity values using TIC for a specific mass range
calibrateIntensity(b, method="TIC", range=c(3000, 5000))
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