I've implemented random forest with both R random forest package and Weka java api. both with same data set (train and test sets are the same) and same configuration (number of trees and mtry). However, the results are different: R - 88.96% (1338 from 1504) accuracy, Weka - 69.28% (1042 from 1504) any suggestion what could make the differences?
Random forests do have a lot of parameters... Are you using the default parameters, or did you set yours ?
My first guess is that you are using default parameters, therefore you have 10 trees in your Weka RF, whereas you have 500 trees with R. This would explain the huge difference in accuracy, in favor of R.
But there can be a lot of other differences as well! The seed may be a problem as well (though the impact will not even compare to the impact of the number of trees), mtry, split criterion, max_depth are to be considered with special care as well.