normalize {crmn}

Normalize a metabolomics dataset

Description

Normalization methods for metabolomics data

Usage

normalize(object, method, segments = NULL, ...)

Arguments

object

an ExpressionSet

method

the desired method

segments

normalization in a cross-validation setup, only to use for validation/QC purposes.

...

passed on to normFit and normPred

Details

Wrapper function for normFit and normPred

Value

the normalized dataset

Author(s)

Henning Redestig

See Also

normFit, normPred

Examples

data(mix)
normalize(mix, "crmn", factor="type", ncomp=3)
#other methods
normalize(mix, "one")
normalize(mix, "avg")
normalize(mix, "nomis")
normalize(mix, "t1")
normalize(mix, "ri")
normalize(mix, "median")
normalize(mix, "totL2")
## can also do normalization with matrices
Y <- exprs(mix)
G <- with(pData(mix), model.matrix(~-1+type))
isIS <- with(fData(mix), tag == "IS")
normalize(Y, "crmn", factor=G, ncomp=3, standards=isIS)