[R] Different results from random.Forest with test option and using predict function

[tdbuskirk]

Hello R Gurus,

I am perplexed by the different results I obtained when I ran code like
this:
set.seed(100)
test1<-randomForest(BinaryY~., data=Xvars, trees=51, mtry=5, seed=200)
predict(test1, newdata=cbind(NewBinaryY, NewXs), type="response")

and this code:
set.seed(100)
test2<-randomForest(BinaryY~., data=Xvars, trees=51, mtry=5, seed=200,
xtest=NewXs, ytest=NewBinarY)

The confusion matrices for the two forests I thought would be the same by
virtue of the same seed settings, but they differ as do the predicted values
as well as the votes.  At first I thought it was just the way ties were
broken, so I changed the number of trees to an odd number so there are no
ties anymore.  

Can anyone shed light on what I am hoping is a simple oversight?  I just
can't figure out why the results of the predictions from these two forests
applied to the NewBinaryYs and NewX data sets would not be the same.

Thanks for any hints and help.

Sincerely,

Trent Buskirk



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