[BioC] error using random forest

Martin Morgan mtmorgan at fhcrc.org
Mon Mar 5 19:03:56 CET 2012

On 03/05/2012 09:43 AM, Salwa Eid wrote:
> Dear all,    Have tried using random forest for classfication and this is the code i wrote exactly: trial.rf<-randomForest(Type ~., data=trial) where Type is a column and determines the type and the trial is the data matrix.  I keep getting this error: Error in eval (exprs, envir, enclos): object '117_at' not found.  Where 117_at is a name of the first column.  I tried removing this column but it gave me the same error for the next column. Any help? Regards,salwa  		 	   		
> 	[[alternative HTML version deleted]]

It's usually better to post a complete example, sometimes with 
artificial data that still reproduces the error:

 >   m = matrix(runif(100), nrow=20, dimnames=list(NULL, 1:5))
 >  randomForest(`1`~., data=m)
Error in eval(expr, envir, enclos) : object '2' not found

Knowing that symbols starting with digits need to be treated specially 
to be 'legal' (from section 1.8 of RShowDoc("R-intro")), and guessing 
that randomForest is doing something to associate the data with the 
formula, I tried

 > colnames(m) = paste("x", colnames(m), sep="")
 > randomForest(x1~., data=m)

  randomForest(formula = x1 ~ ., data = m)
                Type of random forest: regression
                      Number of trees: 500
No. of variables tried at each split: 1

           Mean of squared residuals: 0.0941123
                     % Var explained: -41.17

randomForest documentation says that 'data' should be a data.frame, so 
perhaps I should have

   df = as.data.frame(m)
   randomForest(x1~., data=df)


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