Hi David,
Thank you so much for the pointer. I get it now. I did try the
str(testSeq_df) and since it gave me more than 2 factors for each column, I
believed that it was fine. I get the point clearly now. Thanks again for all
your help. I really appreciate it.
Sincerely,
vishal
On Sat, Dec 26, 2009 at 8:26 AM, David Winsemius <dwinsem...@comcast.net>wrote:
>
> 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
>
>
--
Vishal Thapar, Ph.D.
Post Doctoral Researcher
Cold Spring Harbor Lab
Williams Bldg
1 Bungtown Road
Cold Spring Harbor, NY - 11724
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