filter.std: Filtering of genes based on their standard deviation.

Description Usage Arguments Value Note Author(s) Examples

View source: R/filter.std.R


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





object of the class ExpressionSet.


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.


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


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


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.


Matthias E. Futschik (


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 

Example output

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,, cbind, colMeans, colSums, colnames,,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax,,
    pmin,, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: e1071
Warning message:
no DISPLAY variable so Tk is not available 
49 genes excluded.
1096 genes excluded.

Mfuzz documentation built on Nov. 1, 2018, 5:03 a.m.