normalise-methods: Normalisation of 'MSnExp', 'MSnSet' and 'Spectrum' objects

In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Description

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.

Arguments

object	An object of class "Spectrum", "Spectrum2", "MSnExp" or "MSnSet".
method	A character vector of length one that describes how to normalise the object. See description for details.
...	Additional arguments passed to the normalisation function.

Methods

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.

Examples

## quantifying full experiment
data(msnset)
msnset.nrm <- normalise(msnset, "quantiles")
msnset.nrm

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: ProtGenerics

Attaching package: ‘ProtGenerics’

The following object is masked from ‘package:stats’:

    smooth


This is MSnbase version 2.16.0 
  Visit https://lgatto.github.io/MSnbase/ to get started.


Attaching package: ‘MSnbase’

The following object is masked from ‘package:base’:

    trimws

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): Thu Dec 10 01:28:23 2020 
 MSnbase version: 1.1.22 

MSnbase documentation built on Jan. 23, 2021, 2 a.m.