Filter Features On Intensity and Variance

Description

Function to filter on intensity and variance as typically used in gene expression studies

Usage

filterVarInt(object, IntCutOff = log2(100), IntPropSamples = 0.25, VarCutOff = 0.5)

Arguments

Details

The intensity filter implies that (by default) the intensity levels must be greater than log2(100) in at least 25 percent of the samples.

The variance filter requires that the features have an interquartile range (IQR) greater than 0.5. Note that the IQR is quite insensitive to outliers such that genes with outlying expression values in a few samples are excluded as long as their overall variation is small.

Value

Object of class ExpressionSet containing only the features that pass the variance and intensity filter.

Author(s)

Willem Talloen

References

Gentleman, R. et al. (2005). Bioinformatics and Computational Biology Solutions using R and BioConductor, New York: Springer.

Goehlmann, H. and W. Talloen (2009). Gene Expression Studies Using Affymetrix Microarrays, Chapman & Hall/CRC, p. 128.

See Also

pOverA, filterfun

Examples

if (require(ALL)){
  data(ALL, package = "ALL")
  fALL <- filterVarInt(ALL)
  fALL
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(a4Base)
Loading required package: grid
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

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

Loading required package: AnnotationDbi
Loading required package: stats4
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Attaching package: 'S4Vectors'

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    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: annaffy
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Loading required package: KEGG.db

KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

Loading required package: mpm
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Attaching package: 'MASS'

The following object is masked from 'package:AnnotationDbi':

    select

Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009

mpm version 1.0-22

Loading required package: genefilter

Attaching package: 'genefilter'

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Loading required package: limma

Attaching package: 'limma'

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Attaching package: 'Matrix'

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Loading required package: foreach
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Attaching package: 'a4Core'

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Loading required package: gplots

Attaching package: 'gplots'

The following object is masked from 'package:multtest':

    wapply

The following object is masked from 'package:IRanges':

    space

The following object is masked from 'package:S4Vectors':

    space

The following object is masked from 'package:stats':

    lowess


a4Base version 1.20.0

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/a4Base/filterVarInt.Rd_%03d_medium.png", width=480, height=480)
> ### Name: filterVarInt
> ### Title: Filter Features On Intensity and Variance
> ### Aliases: filterVarInt
> ### Keywords: manip
> 
> ### ** Examples
> 
> if (require(ALL)){
+   data(ALL, package = "ALL")
+   fALL <- filterVarInt(ALL)
+   fALL
+ }
Loading required package: ALL
ExpressionSet (storageMode: lockedEnvironment)
assayData: 2400 features, 128 samples 
  element names: exprs 
protocolData: none
phenoData
  sampleNames: 01005 01010 ... LAL4 (128 total)
  varLabels: cod diagnosis ... date last seen (21 total)
  varMetadata: labelDescription
featureData: none
experimentData: use 'experimentData(object)'
  pubMedIds: 14684422 16243790 
Annotation: hgu95av2 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>