[BioC] Questions regarding MCRestimate package

[Stella S [guest]]

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

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