[BioC] About CLAC package

[Matthew Keller]

Hi Allen,

I have never used CLAC before, but if you read the error message,
you'll see that somewhere, the function max() is being called on a
factor. Try traceback(), which might tell you where max is being
called. Better yet, check over the classes of your data to make sure
that you don't have a factor where you're expecting a numeric. R has
(in my opinion) an annoying default s.t. strings are interpreted as
factors when data is read in. You can change this default  behavior
(check out the options() function), or just change the classes one at
a time using as.numeric()...

Matt

On Nov 10, 2007 9:36 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, targetF iDR=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
>
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-- 
Matthew C Keller
Asst. Professor of Psychology
University of Colorado at Boulder
www.matthewckeller.com