MSnExp
, MSnSet
and Spectrum
objectsnormalise-methods.Rd
The normalise
method (also available as normalize
)
performs basic normalisation on spectra
intensities of single spectra ("Spectrum"
or
"Spectrum2"
objects),
whole experiments ("MSnExp"
objects) or
quantified expression data ("MSnSet"
objects).
Raw spectra and experiments are normalised using max
or
sum
only. For MSMS spectra could be normalised to their
precursor
additionally. Each peak intensity is divided by the
highest intensity in the spectrum, the sum of intensities or the intensity
of the precursor.
These methods aim at facilitating relative peaks heights between
different spectra.
The method
parameter for "MSnSet"
can be
one of sum
, max
, quantiles
, center.mean
,
center.median
, .median
, quantiles.robust
or
vsn
. For sum
and max
, each feature's reporter
intensity is divided by the maximum or the sum respectively. These two
methods are applied along the features (rows).
center.mean
and center.median
translate the respective
sample (column) intensities according to the column mean or
median. diff.median
translates all samples (columns) so that
they all match the grand median. Using quantiles
or
quantiles.robust
applies (robust) quantile normalisation, as
implemented in normalize.quantiles
and
normalize.quantiles.robust
of the preprocessCore
package. vsn
uses the vsn2
function from the
vsn
package. Note that the latter also glog-transforms the
intensities. See respective manuals for more details and function
arguments.
A scale
method, mimicking the base scale
method exists
for "MSnSet"
instances. See
?base::scale
for details.
The normalise
methods:
signature(object = "MSnSet", method = "character")
Normalises the object
reporter ions intensities using
method
.
signature(object = "MSnExp", method = "character")
Normalises the object
peak intensities using
method
.
signature(object = "Spectrum", method = "character")
Normalises the object
peak intensities using
method
.
signature(object = "Spectrum2", method = "character",
precursorIntensity)
Normalises the object
peak intensities using
method
. If method == "precursor"
,
precursorIntensity
allows to specify the intensity of the
precursor manually.
The scale
method:
signature(x = "MSnSet", center = "logical", scale =
"logical")
See ?base::scale
.
## quantifying full experiment
data(msnset)
msnset.nrm <- normalise(msnset, "quantiles")
msnset.nrm
#> MSnSet (storageMode: lockedEnvironment)
#> assayData: 55 features, 4 samples
#> element names: exprs
#> protocolData: none
#> phenoData
#> sampleNames: iTRAQ4.114 iTRAQ4.115 iTRAQ4.116 iTRAQ4.117
#> varLabels: mz reporters
#> varMetadata: labelDescription
#> featureData
#> featureNames: X1 X10 ... X9 (55 total)
#> fvarLabels: spectrum ProteinAccession ... collision.energy (15 total)
#> fvarMetadata: labelDescription
#> experimentData: use 'experimentData(object)'
#> Annotation: No annotation
#> - - - Processing information - - -
#> Data loaded: Wed May 11 18:54:39 2011
#> iTRAQ4 quantification by trapezoidation: Wed Apr 1 21:41:53 2015
#> Normalised (quantiles): Wed Sep 11 07:30:37 2024
#> MSnbase version: 1.1.22