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]