[BioC] Questions regarding MCRestimate package
Stella S [guest]
guest at bioconductor.org
Wed Aug 1 20:47:19 CEST 2012
I'm currently using MCRestimate package and I have a question regarding the MCRestimate function.
Here is my code:
NestedCV.rf<-MCRestimate(eset, "Class", classificatin.fun="RF.wrap",
I'm pretty sure that I was providing "eset" and "Class" correctly. But I was always getting a warning message:
may be at least one parameter in the parameter list that does not correspond to a parameter of the classification or any preprocessing function.
When I removed "mtry=c(10,50)", it worked well without giving any warning message. So it seems that it was the "mtry" that led to that warning message. However, when I removed "var.numbers=c(100)" and left "mtry=c(10,50) only, it worked well also.
I found the information on Bioconductor Code
Search:Template.R/MCRestimate/inst/scripts/Template.R, see following:
Package: MCRestimate - Version: 2.13.0 - Language: r
the.expression.set <- get(load(DataSet))
r.forest <- MCRestimate(the.expression.set,
So it seems that specifying both "mtry" and "var.numbers" for RF.wrap is allowed.
Could anyone please help me figure out what's going on here? Thanks very much.
-- output of sessionInfo():
MCRestimate_2.12.0 biobase_2.16.0 randomForest_4.6-6 e1071_1.6
Sent via the guest posting facility at bioconductor.org.
More information about the Bioconductor