[BioC] mtry in randomForest

Liu, Xin Xin.Liu at arragen.com
Fri Jul 2 14:45:38 CEST 2004

Hello group,

I created an Expression Set as the following:

Expression Set (exprSet) with 
        4986 genes
        12 samples
                 phenoData object with 2 variables and 12 cases
                cov1: Genotype
                cov2: Treatment

then I run the Rondom Forest:
rf <- randomForest(Xm, trainY, ntree = 2000, mtry = 70, importance = TRUE)
var.imp.plot(rf, n.var = 30)

The problem is when I chose different mtry, such as mtry = 70, mtry = 65, and mtry = 60, I got totally different gene lists with importance. Really get confusing.

Any suggestions? Thank you.


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