MALDIquant (version 1.1)

calibrateIntensity-methods: Calibrates intensities of a MassSpectrum object.

Description

This function calibrates (normalize) intensities of MassSpectrum objects.

Usage

## S3 method for class 'MassSpectrum':
calibrateIntensity(object,
  method=c("TIC", "PQN", "median"), ...)
## S3 method for class 'list':
calibrateIntensity(object,
  method=c("TIC", "PQN", "median"), ...)

Arguments

object

MassSpectrum object or a list of MassSpectrum objects.

method

the calibration method to be used. This should be one of "TIC", "PQN" or "median". See Details section.

...

arguments to be passed to other functions. Currently only range is for method="TIC" is supported. If object is a list mc.cores is also supported.

Value

• Returns a modified MassSpectrum object with calibrated intensities.

Details

A number of different calibration methods are provided: [object Object],[object Object] "Median":{The median of intensities of a MassSpectrum object is set to one.}

References

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): 4281-4290.

See Also

MassSpectrum

Website: http://strimmerlab.org/software/maldiquant/

Examples

## 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))