Hi there, I have trying to run the vsn normalization function, and it reported error:
Error: could not find function "normalize.AffyBatch.vsn"
Can anyone help me out with this?

normalize.AffyBatch.methods()
[1] "constant"         "contrasts"        "invariantset"     "loess"            "methods"          "qspline"          "quantiles"       
[8] "quantiles.robust" "vsn" 
myData.VSN <- normalize.AffyBatch.vsn(myData)
Error: could not find function "normalize.AffyBatch.vsn"

What is going on?

That function isn't really available for the affy package any longer, and has been superceded by rmavsn, which will background correct and normalize using vsn2, and then perform medianpolish to generate summarized expression values. We should probably just strip out vsn from normalize.AffyBatch.methods to remove this confusion.

If you just want the background corrected and normalized data you could do

normdat <- 2^exprs(vsn2(<yourAffyBatchgoeshere>))

or if you want RMA expression values with vsn background correction, then

eset <- rmavsn(<yourAffyBatchgoeshere>)