### Name: vsn
### Title: Variance stabilization and calibration for microarray data.
### Aliases: vsn
### Keywords: robust

### ** Examples

data(kidney)
log.na = function(x) log(ifelse(x>0, x, NA))

if(interactive()) {
  x11(width=9, height=4.5)
  par(mfrow=c(1,2))
}
plot(log.na(exprs(kidney)), pch=".", main="log-log")

vsnkid = vsn(kidney)   ## transform and calibrate
plot(exprs(vsnkid), pch=".", main="h-h")

if (interactive()) {
  x11(width=9, height=4)
  par(mfrow=c(1,3))
}

meanSdPlot(vsnkid)
vsnPlotPar(vsnkid, "factors")
vsnPlotPar(vsnkid, "offsets")

## this should always hold true
params = preproc(description(vsnkid))$vsnParams
stopifnot(all(vsnh(exprs(kidney), params) == exprs(vsnkid)))