Question: Questions regarding MCRestimate package
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7.0 years ago by
Guest User12k
Guest User12k wrote:
Hello, 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", variableSel.fun="varSel.highest.var", poss.parameters= list(var.numbers=c(100), mtry=c(10,50), cross.outer=10,cross.inner=10,cross.repeat=3) I'm pretty sure that I was providing "eset" and "Class" correctly. But I was always getting a warning message: InMCRestimate.default(eset,"Class",classification.fun="RF.wrap",: There 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 library(MCRestimate) library(randomForest) library(pamr) library(e1071) the.expression.set <- get(load(DataSet)) if(RF){ list.of.parameter <- c(list(mtry=mtry.range,ntree=ntree.range),parameter.for.preprocessing) r.forest <- MCRestimate(the.expression.set, class.colum, classification.fun="RF.wrap", poss.parameters=list.of.parameter, thePreprocessingMethods=thePreprocessingfunktionsRF, cross.outer=cross.outer, cross.inner=cross.inner, cross.repeat=cross.repeat, reference.class=ref.class, plot.label=plot.label, rand=SEED) save(r.forest, file=paste("backRF",SEED,".RData",sep="")) } 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. Sincerely, Stella -- 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.
classification mcrestimate • 518 views
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