Mfuzz: standardise2 – R documentation

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standardise2

Standardization in regards to selected time-point

Description

Standardisation of the expression values of every gene is performed, so that the expression values at a chosen time point are zero and the standard deviation of expression profiles of individual genes/transcripts/proteins is one.

Usage

standardise2(eset,timepoint=1)

Arguments

`eset`	object of the class ExpressionSet.
`timepoint`	integer: which time point should have expression values of zero.

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 standardise2 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 <- standardise2(yeastF,timepoint=1)

# 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