filterVarInt: Filtering on Intensity and Variance

In a4Base: Automated Affymetrix Array Analysis Base Package

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

object	ExpressionSet object
IntCutOff	cut-off value used for the intensity filt
IntPropSamples	proportion of samples used by the intensity filter; by default IntPropSamples is set to 0.25.
VarCutOff	cut-off value used for the variance filter

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
}

a4Base documentation built on Nov. 8, 2020, 5:41 p.m.