vst {lumi} | R Documentation |
Stabilizing the expression variance based on the bead level expression variance and mean relations
vst(u, std, nSupport = min(length(u), 500), method = c('iterate', 'quadratic'), ifPlot = FALSE)
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 |
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.
Return the transformed (variance stabilized) expression values.
Pan Du, Simon Lin
Lin, S.M., Du, P., Kibbe, W.A., "Model-based Variance-stabilizing Transformation for Illumina Mi-croarray Data", submitted
## 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)