[R] how to tabulate the prediction value using table function for naive baiyes in R

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Jun 30 21:44:12 CEST 2010


On Wed, Jun 30, 2010 at 11:44 AM, Aadhithya <sistaadhi at gmail.com> wrote:
> Hi,
> I have written a code in R for classifying microarray data using naive
> bayes, the code is given below:
> library(e1071)
> train<-read.table("Z:/Documents/train.txt",header=T);
> test<-read.table("Z:/Documents/test.txt",header=T);
> cl <- c(c(rep("ALL",10), rep("AML",10)));
> cl <- factor(cl)
> model <- naiveBayes(train,cl);
> pred<-predict(model,test,type = "raw");
> table(pred,cl);

Do you expect the predicted labels on your testing data to be the same
labels you used from your training data?

> everything is working fine I am able to build the model and predict also but
> I am not able to get the confusion matrix using table function.its giving me
> the following error when I execute the line "table(pred,cl)"
> Error in table(pred,cl):all arguments must have the same length
> I am not sure where I am going wrong.

Here's a piece of advice you might want to consider: stop driving blindly.

The error tells you where you are going wrong, so take some time to
read it a bit more closely. Then take another minute or two to see
what your "pred" and "cl" vectors look like.

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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