standardise: Standardization of expression data for clustering.

Description Usage Arguments Value Note Author(s) Examples

View source: R/standardise.R

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

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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

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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 documentation built on Nov. 17, 2017, 10:06 a.m.