Authors Marie Tremblay-Franco (marie.tremblay-franco@toulouse.inra.fr) and Marion Landi (marion.landi@clermont.inra.fr): MetaboHUB: The French National Infrastructure for Metabolomics and Fluxomics (http://www.metabohub.fr/en)

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.

NMR Normalization

Description

Normalization (operation applied on each individual spectrum) of bucketed and integrated NMR data

Workflow position

Upstream tools

Name	output file	format	parameter
NMR_Bucketing	NMR_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 bucketed and integrated NMR 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

bucketedData.tsv: tabular output

Data matrix with p rows (buckets) and n columns (samples) containing the intensities
sampleMetadata.tsv: tabular output

sampleMetadata file identical to the file given as argument if "PQN" or "Quantitative" normalization method; file with n rows (samples) and 2 columns containing sample identifier (rownames) and sample order if "None" or "Total" normalization methof

Mandatory file in the statistical analysis step of the workflow
variableMetadata.tsv: tabular output

file with p rows (buckets) and 2 columns containing variable identifier (rownames) and bucket order. Can add columns with numeric and/or character variable metadata.

Mandatory file in the statistical analysis step of the workflow
spectra.pdf: pdf output

Graphical chart of bucketed and integrated data

Working example

Under construction

/repository/static/images/695f5b3e6965260a/.%2Fstatic%2Fimages%2FMth_Travaux.png