[R] Help with SVM package Kernlab

[David Winsemius]

On Dec 26, 2009, at 3:53 AM, Vishal Thapar wrote:

> Hi All,
>
> Thank you for your replies so far. I was hoping I could get some  
> more input from you on this issue. It seems to me that I have hit a  
> dead end here and would really appreciate some feedback. I have  
> followed all the suggestions you have mentioned but they still this  
> is stuck. Earlier I thought that it was a "factor" issue but now  
> even that is not the error. Here is the script and the error. Thanks  
> for your help. I have attached the sample test file as well as the  
> training file in case you would like to run it locally.
> ---------------------------------
> library(seqinr)
> library("kernlab")


 > str(mars500_1_df)
'data.frame':	256 obs. of  501 variables:
All of which are factors with 4 levels

> testSeq_fa=read.fasta("temp1.fasta")
> testSeq_seq=t(getSequence(testSeq_fa))
> testSeq_df=as.data.frame(testSeq_seq,stringsAsFactors=FALSE)
> testSeq_df = cbind(Class="-",testSeq_df)
> testSeq_df = data.frame(lapply(testSeq_df,factor))
 > str(testSeq_df)
'data.frame':	20 obs. of  501 variables:

$ V9   : Factor w/ 3 levels "a","c","t": 2 1 2 1 3 2 3 2 3 1 ...
$ V9   : Factor w/ 3 levels "a","c","t": 2 1 2 1 3 2 3 2 3 1 ...
$ V26  : Factor w/ 3 levels "a","g","t": 2 1 1 1 1 3 1 3 1 3 ...
...and about 10 more...

So I think you were closer but not quite there yet.
 > for(i in 11:501){if (length(levels(testSeq_df[,i])) == 3)
                 levels(testSeq_df[,i])<- c(a="a",g="g",c="c",c="t")}

 > predict(mars500_1,testSeq_df)
  [1] - - - - + - + - - - - + + + - - - - - +
Levels: - +

YES, it WAS (and still is) a "factor issue". You were shown how to  
look at objects with str. Why have you not adopted the practice?

--

David Winsemius, MD
Heritage Laboratories
West Hartford, CT