Filter Features On Intensity and Variance
Function to filter on intensity and variance as typically used in gene expression studies
filterVarInt(object, IntCutOff = log2(100), IntPropSamples = 0.25, VarCutOff = 0.5)
cut-off value used for the intensity filter
proportion of samples used by the intensity
filter; by default
cut-off value used for the variance filter
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.
Object of class ExpressionSet containing only the features that pass the variance and intensity filter.
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.
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