standardise2: Standardization in regards to selected time-point

Description Usage Arguments Value Note Author(s) Examples

View source: R/standardise2.R

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

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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

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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 documentation built on May 31, 2017, 10:59 a.m.