Filtering of genes based on their standard deviation.

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Description

This function can be used to exclude genes with low standard deviation.

Usage

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filter.std(eset,min.std,visu=TRUE)

Arguments

eset

object of the class ExpressionSet.

min.std

threshold for minimum standard deviation. If the standard deviation of a gene's expression is smaller than min.std the corresponding gene will be excluded.

visu

If visu is set to TRUE, the ordered standard deviations of genes' expression values will be plotted.

Value

The function produces an object of the ExpressionSet class. It is the same as the input eset object, except for the genes excluded.

Note

As soft clustering is noise robust, pre-filtering can usually be avoided. However, if the number of genes with small expression changes is large, such pre-filtering may be necessary to reduce noise.

Author(s)

Matthias E. Futschik (http://itb.biologie.hu-berlin.de/~futschik)

Examples

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data(yeast) # data set includes 17 measurements
yeastF <- filter.NA(yeast) # filtering of genes based on missing values 
yeastF <- filter.std(yeastF,min.std=0.3) # filtering of genes based on standard deviation 

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