normalizeIntensity: Normalize Intensity

In CeMOS-Mannheim/moleculaR: Spatial Probabilistic Mapping of Metabolite Ensembles in Mass Spectrometry Imaging

Normalize Intensity

Description

This normalizes spectral intensities based on a number of different methods.

Usage

normalizeIntensity(x, method, meanMethod = "mean", mz = NULL, tol = NULL)

Arguments

x:	a list of MassPeaks objects.
method:	the normalization method, has to be one of c('medianFoldChange', 'RMS', 'TIC', 'median', 'IS').
meanMethod:	only used for 'medianFoldChange' normalization. See ?MALDIquant::mergeMassPeaks for more info.
mz:	a numeric, the m/z value of the internal standard (IS) - only relevant for ‘method=’IS''.
tol:	a numeric, the absolute tolerance for m/z (in Da) - only relevant for ‘method=’IS''.

Details

The 'medianFoldChange' normalization is done such that for every spectrum a median fold-change of peak intensities is calculated with reference to the mean spectrum which is then taken as a normalization factor for that particular spectrum (see reference [1]). The 'RMS', 'TIC' and 'median' normalization methods are equivalent to their counterparts in other packages (ex. MALDIquant), they are just adapted to process centroided data of 'MassPeak' Objects. Note that for 'medianFoldChange' normalization, it is important to run peak binning beforehand. The 'IS' method assumes the presence of an internal standard at 'mz' m/z against which all intensities are normalized (pixel-wise).

Value

Intensity-normalized list of MassPeaks objects.

References

1. Veselkov, Kirill, et al. "BASIS: High-performance bioinformatics platform for processing of large-scale mass spectrometry imaging data in chemically augmented histology." Scientific reports 8.1 (2018): 1-11. 2. Deininger, Sören-Oliver, et al. "Normalization in MALDI-TOF imaging datasets of proteins: practical considerations." Analytical and bioanalytical chemistry 401.1 (2011): 167-181.

CeMOS-Mannheim/moleculaR documentation built on April 14, 2025, 8:27 a.m.