vst {lumi} | R Documentation

## Variance Stabilizing Transformation

### Description

Stabilizing the expression variance based on the bead level expression variance and mean relations

### Usage

    vst(u, std, nSupport = min(length(u), 500), method = c('iterate', 'quadratic'), ifPlot = FALSE)

### Arguments

`u` | mean expression of the beads with same sequence
`std` | expression standard deviation of the beads with same sequence
`nSupport` | the number of down-sampling to speed processing
`method` | methods of fitting the relations between expression variance and mean relations
`ifPlot` | plot intermediate results or not

### Details

The variance-stabilizing transformation (VST) takes the advantage of larger number of technical replicates available on the Illumina microarray. It models the mean-variance relationship of the within-array technical replicates at the bead level of Illumina microarray. An arcsinh transform is then applied to stabilize the variance. See reference for more details.

### Value

Return the transformed (variance stabilized) expression values.

### Author(s)

Pan Du, Simon Lin

### References

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

### See Also

`lumiT`, `inverseVST`

### 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 variance stabilizing transform with plotting intermediate result
    transformedU <- vst(u, std, ifPlot=TRUE)

[Package lumi version 1.2.0 Index]