Mfuzz: standardise – R documentation

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standardise

Standardization of expression data for clustering.

Description

Standardisation of the expression values of every gene/transcript/protein is carried out, so that the average expression value for each gene/transcript/protein is zero and the standard deviation of its expression profile is one.

Usage

standardise(eset)

Arguments

eset

object of the classe ExpressionSet.

Value

The function produces an object of the ExpressionSet class with standardised expression values.

Note

Mfuzz assumes that the given expression data are preprocessed (including the normalisation). The function standardise does not replace the normalisation step. Note the difference: Normalisation is carried out to make different samples comparable, while standardisation (in Mfuzz) is carried out to make transcripts (genes) comparable.

Author(s)

Matthias E. Futschik (http://www.sysbiolab.eu)

Examples

if (interactive()){
data(yeast)
# Data pre-processing
yeastF <- filter.NA(yeast)
yeastF <- fill.NA(yeastF)
yeastF <- standardise(yeastF)

# Soft clustering and visualisation
cl <- mfuzz(yeastF,c=20,m=1.25)
mfuzz.plot(yeastF,cl=cl,mfrow=c(4,5))
}

Mfuzz

Soft clustering of time series gene expression data

v2.50.0

GPL-2

Authors

Matthias Futschik <matthias.futschik@sysbiolab.eu>

Initial release

2016-10-18