Question: Questions regarding MCRestimate package
gravatar for Guest User
6.8 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","RF.wrap","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","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,"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
classification mcrestimate • 493 views
ADD COMMENTlink written 6.8 years ago by Guest User12k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 133 users visited in the last hour