inverseVST {lumi}R Documentation

Inverse VST transform

Description

Inverse transform of VST (variance stabilizing transform), see vst.

Usage

inverseVST(x, fun = c('asinh', 'log'), parameter)

Arguments

x a vector of VST transformed data
fun function used in VST transform
parameter parameter of VST function

Details

Recover the raw data from VST transformed data returned by vst.

Value

Return the raw data before VST transform

Author(s)

Pan Du

References

Lin, S.M., Du, P., Kibbe, W.A., "Model-based Variance-stabilizing Transformation for Illumina Mi-croarray Data", submitted

See Also

vst

Examples


## load example data
data(example.lumi)

## get the gene expression mean for one chip
u <- exprs(example.lumi)[,1]
## get the gene standard deviation for one chip
std <- se.exprs(example.lumi)[,1]

## do variance stabilizing transform
transformedU <- vst(u, std)

## do inverse transform and recover the raw data
parameter <- attr(transformedU, 'parameter')
transformFun <- attr(transformedU, 'transformFun')
recoveredU <- inverseVST(transformedU, fun=transformFun, parameter=parameter)

## compare with the raw data
print(u[1:5])
print(recoveredU[1:5])


[Package lumi version 1.2.0 Index]