Question: Error: could not find function "normalize.AffyBatch.vsn"
0
gravatar for billchenxi
2.6 years ago by
billchenxi0
billchenxi0 wrote:

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?

 

 

 

 

 

 

vsn • 1.2k views
ADD COMMENTlink modified 2.6 years ago by James W. MacDonald51k • written 2.6 years ago by billchenxi0
Answer: Error: could not find function "normalize.AffyBatch.vsn"
0
gravatar for James W. MacDonald
2.6 years ago by
United States
James W. MacDonald51k wrote:

That function isn't really available for the affy package any longer, and has been superceded by rmavsn, which will background correct and normalize using vsn2, and then perform medianpolish to generate summarized expression values.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>)

 

ADD COMMENTlink written 2.6 years ago by James W. MacDonald51k

What is the difference between the justvsn() and the above functions?
Thanks.

 

ADD REPLYlink written 2.6 years ago by billchenxi0

Are you saying that the help pages for these functions are not clear? If so, will you please say what part you don't understand, so the maintainer has an idea how to clarify?
 

ADD REPLYlink written 2.6 years ago by James W. MacDonald51k
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