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 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)

[Package lumi version 2.40.0 Index]