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Normalization (version 1.0.7)
Default method is total intensity
Select 'None' for no representation,'Overlay' to overlay all spectra on a unique chart and 'One per individual' to generate an individual chart for each observation
Authors Marie Tremblay-Franco (marie.tremblay-franco@inra.fr) and Marion Landi (marion.landi@clermont.inra.fr)
MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (https://www.metabohub.fr/home.html)

Please cite

F. Dieterle, A. Ross, G. Schlotterbeck, and H. 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.

Normalization

Description

Normalization (operation applied on each (preprocessed) individual spectrum) of preprocessed data

Workflow position

Upstream tools

Name output file format parameter
NMR_Bucketing Normalization_bucketedData.tsv tabular Ions Matrix

Downstream tools

Name Output file Format
Univariate variableMetadata.tsv Tabular
Multivariate sampleMetadata.tsv Tabular
  variableMetadata.tsv Tabular

Input files

Parameter : num + label Format
DataMatrix Tabular

DataMAtrix

variable x sample dataMatrix tabular separated file containing (preprocessed) spectra, with . as decimal, and NA for missing values

Parameters

DataMatrix
see "Input files" section above

Normalization method
normalization to apply on each spectrum:
Name Normalization
None No
Total Total intensity
PQN Probabilistic Quotient Normalization
QuantitativeVariable Weight, osmolality, ...
sampleMetadata
sample x metadata sample tabular separated file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
Mandatory for "PQN" or "Quantitative" normalization method
The row names must be identical to the column names of the dataMatrix file

Spectra representation:
Graphical chart of bucketed and integrated raw files
If "Overlay": the n (sample number) spectra are overlaid on the same figure
If "One_per_individual": pdf file includes n pages (1 per sample)

Output files

dataMatrix.tsv
tabular output
Data matrix with p rows (variable) and n columns (samples) containing the intensities

spectra.pdf
pdf output
Graphical chart of bucketed and integrated data

Working example

Under construction

/repository/static/images/91f28cbb28622fc9/.%2Fstatic%2Fimages%2FMth_Travaux.png

Changelog/News

Version 1.0.7 - 25/09/2018

  • Bug fixing for PQN normalization in case of zero's

Version 1.0.3 - 30/01/2017

  • BUGFIX: Fix a bug: stack overflow for integers

Version 1.0.2 - 22/10/2016

  • NEW: this tool was previously named NMR Normalization. It had been generalize to deal with all kind of preprocessed data

Version 1.0.1 - 14/04/2016

  • TEST: refactoring to pass planemo test using conda dependencies

Version 2015-01-28 - 28/01/2015