inverseVST: Inverse VST transform

In lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays

Description

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

Usage

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

Arguments

x	a VST transformed LumiBatch object or a numeric matrix or vector
fun	function used in VST transform
parameter	parameter of VST function

Details

Recover the raw data from VST transformed data returned by vst. This function can be directly applied to the VST transformed or VST + RSN normalized LumiBatch object to reverse transform the data to the original scale.

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])

## do inverse transform of the VST + RSN processed data
lumi.N <- lumiExpresso(example.lumi[,1:2])
## Inverse transform. 
## Note: as the normalization is involved, the processed data will be different from the raw data.
lumi.N.raw <- inverseVST(lumi.N)

lumi documentation built on Nov. 8, 2020, 5:27 p.m.