Zero difference in Gini Importance Index across repeats

[Paul o Reilly]

Hi,

I am trying to use jungle to construct a expression signature capable of predicting phenotype, in this case whether cells will be sensitive or resistant to drug treatment. I am attempting to optimize the area under the curve of the random jungle (generated from prediction of phenotype on a test set) by the backward elimination of variables. 

I generate the jungle a number of times treating these as "replicates". During my brief foray with the randomForest package I saw differences in Gini Importance Index scores and sometimes small differences in the ranked position of the variable between repeats. However when I take the same approach in jungle I see zero difference between Gini importance values. Do I need to set different seeds ? Is this even a problem ?

Thanks in advance for any help given

Paul