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Hi James, try: data=list(x=x,y=y, geneid=as.character(1:nrow(x)),genenames=paste("g",as.character(1:nrow (x)),sep=""), logged2=TRUE) see what happens. JP- --On Wednesday, October 04, 2006 6:41 PM -0700 James Anderson <janderson_net at="" yahoo.com=""> wrote: > Hi, > Has anybody used the SAM R package? I followed the pdf of the > instruction and try to use the examples on the pdf file to test the code. > However, I am having a problem with running the code, below is the code I > am running: > > > library(samr) > set.seed(100) > > x<-abs(matrix(rnorm(1000*20),ncol=20)) > dd<-sample(1:1000,size=100) > u<-matrix(2*rnorm(100),ncol=10,nrow=100) > x[dd,11:20]<-x[dd,11:20]+u > y<-c(rep(1,10),rep(2,10)) > data=list(x=x,y=y,geneid=as.character(1:nrow(x)),genenames=paste("g" ,as.c > haracter(1:nrow(x)))) samr.obj = samr(data, resp.type="Two class > unpaired", nperms=100) > > I don't have any problem until the last line, when I was running the last > line, it complains: > > perm= 1 > Error in if (logged2) { : argument is of length zero > > I don't know what's wrong, I copied the code from the pdf file and run > it. It supposed to run. Does anybody know how to solve this problem? > > Many thanks, > James > > > --------------------------------- > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 ################################## Jianping Jin Ph.D. Bioinformatics scientist Center for Bioinformatics Room 3133 Bioinformatics building CB# 7104 University of Chapel Hill Chapel Hill, NC 27599 Phone: (919)843-6105 FAX: (919)843-3103 E-Mail: jjin at email.unc.edu