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

Hi, Please read the posting guide, that is perhaps the best advice that can be given which will tell you among other things to provide the output of sessionInfo, and to provide a reproducible example. The second best advice is to include a signature that identifies you. There are a number of people who will not respond to anonymous emails, so if you want their help you will need to identify yourself. best wishes Robert affy snp 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Matthew C Keller Asst. Professor of Psychology University of Colorado at Boulder www.matthewckeller.com

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 >