[BioC] About CLAC package

[affy snp]

Dear list,

Hello! My name is Allen Shore, a graduate student at Wistar Institute
in Philadelphia. I was trying CLAC to analyze Affy SNP 250K array to
call gain and loss. The data set consists of 238304 rows (snp probes)
and 243 columns (samples).

I tried clac.preparenormal.R() first and got an error message which is:

> NormalResult<-clac.preparenormal.R(cghlog2[,1:47], cghlog2[,48:243], Normal.Type=rep(0,196), chromosome.number=B[,1], nucleotide.position=B[,2], windowsize=5, targetFDR=0.01, chromosomeOption=FALSE)
Error in Summary.factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  :
 max not meaningful for factors

I tried it one more time and the process was killed. I have no idea
what the reason could be.

> NormalResult<-clac.preparenormal.R(cghlog2[,1:47], cghlog2[,48:243], Normal.Type=rep(0,196), chromosome.number=B[,1], nucleotide.position=B[,2], windowsize=5, targetFDR=0.01, chromosomeOption=FALSE)
Killed
-bash-3.00$

Does anybody has experience with CLAC? Any suggestions would be
appreciated!

Sincerely,
       Allen



On Nov 10, 2007 11:36 AM, affy snp <affysnp at gmail.com> wrote:
> Dear list,
>
>
>
> I was trying CLAC to analyze Affy SNP 250K array to call gain and
> loss. The data set consists of 238304 rows (snp probes) and 243
> columns (samples).
>
> I tried clac.preparenormal.R() first and got an error message which is:
>
> > NormalResult<-clac.preparenormal.R(cghlog2[,1:47], cghlog2[,48:243], Normal.Type=rep(0,196), chromosome.number=B[,1], nucleotide.position=B[,2], windowsize=5, targetFDR=0.01, chromosomeOption=FALSE)
> Error in Summary.factor(c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L,  :
>   max not meaningful for factors
>
> Do you have any idea about this? I am new to R and bioconductor so any help
> will be appreciated!
>
> Sincerely,
>        Allen
>