normFit {crmn}R Documentation

Fit a normalization model

Description

Fit the parameters for normalization of a metabolomics data set.

Usage

normFit(object, method, one="Succinate_d4", factors, lg=TRUE,
    fitfunc=lm, ...)

Arguments

object an ExpressionSet or a matrix (with samples as columns) in which case the standards must be passed on via ...
method chosen normalization method
one single internal standard to use for normalization
factors column names in the pheno data slot describing the biological factors. Or a design matrix directly.
lg logical indicating that the data should be log transformed
fitfunc the function that creates the model fit for normalization, must use the same interfaces as lm.
... passed on to standardsFit, standards, analytes

Details

Normalization is first done by fitting a model and then applying that model either to new data or the same data using normPred. Five different methods are implemented.

t1
divide by row-means of the L_2 scaled internal standards
one
divide by value of a single, user defined, internal standard
totL2
divide by the square of sums of the full dataset
nomis
See Sysi-Aho et al.
crmn
See Redestig et al.

Value

a normalization model

Author(s)

Henning Redestig henning@psc.riken.jp

References

Sysi-Aho, M.; Katajamaa, M.; Yetukuri, L. & Oresic, M. Normalization method for metabolomics data using optimal selection of multiple internal standards. BMC Bioinformatics, 2007, 8, 93

Redestig, H.; Fukushima, A.; Stenlund, H.; Moritz, T.; Arita, M.; Saito, K. & Kusano, M. Compensation for systematic cross-contribution improves normalization of mass spectrometry based metabolomics data Anal Chem, 2009, 81, 7974-7980

See Also

normPred, standards, model.matrix

Examples

data(mix)
nfit <- normFit(mix, "crmn", factors="type", ncomp=3)
slplot(sFit(nfit)$fit$pc, scol=as.integer(mix$runorder))
## same thing
Y <- exprs(mix)
G <- model.matrix(~-1+mix$type)
isIS <- fData(mix)$tag == 'IS'
nfit <- normFit(Y, "crmn", factors=G, ncomp=3, standards=isIS)
slplot(sFit(nfit)$fit$pc, scol=as.integer(mix$runorder))

[Package crmn version 0.0.11 Index]