Hi there: I tried to run SAM for one-class case , using package siggenes. (R 1.9.1, siggenes Version: 1.0.6) My data set contains 2000 genes with 4 replications. I got the following error message: -------------------------- Warning: There are 2000 genes which have variance Zero or no non- missing values. The d-value of these genes is set to NA. Error in var(v) : missing observations in cov/cor -------------------------------- I checked siggenes vignette, they didn't out down any example for one-class study. I tried to use the data(golub)(used as example in the vignette) to do one-sample case as following ------------------------------------- > temp=sam(golub[,1:10],golub.cl[1:10],rand=123) SAM Analysis for the one-class case. Warning: Expected classlabel is 1. cl will thus be set to 1. Warning: There are 1041 genes which have variance Zero or no non- missing values. The d-value of these genes is set to NA. Error in var(v) : missing observations in cov/cor ---------------------------- Although this is not an appropriate data set for one-class study, but SAM should still work. Anybody has idea about this, I would appreciate for any hint. BTW, I used Excel SAM program before, it was OK for this kind one- class study. Thank you all! Fangxin -- Fangxin Hong, Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong@salk.edu

I check the source code, I found a bug in function xy.cal, line 19 x<-rep(1,length(cl)) should be x<-which(cl==1) Any idea? I think that is the reason. Fangxin > Hi there: > I tried to run SAM for one-class case , using package siggenes. > (R 1.9.1, siggenes Version: 1.0.6) > > My data set contains 2000 genes with 4 replications. I got the following > error message: > -------------------------- > Warning: There are 2000 genes which have variance Zero or no non- missing > values. > The d-value of these genes is set to NA. > > Error in var(v) : missing observations in cov/cor > -------------------------------- > I checked siggenes vignette, they didn't out down any example for > one-class study. I tried to use the data(golub)(used as example in the > vignette) to do one-sample case as following > ------------------------------------- >> temp=sam(golub[,1:10],golub.cl[1:10],rand=123) > SAM Analysis for the one-class case. > > Warning: Expected classlabel is 1. cl will thus be set to 1. > > Warning: There are 1041 genes which have variance Zero or no non- missing > values. > The d-value of these genes is set to NA. > > Error in var(v) : missing observations in cov/cor > ---------------------------- > Although this is not an appropriate data set for one-class study, but SAM > should still work. Anybody has idea about this, I would appreciate for any > hint. > BTW, I used Excel SAM program before, it was OK for this kind one- class > study. > > Thank you all! > Fangxin > > > > > -- > Fangxin Hong, Ph.D. > Plant Biology Laboratory > The Salk Institute > 10010 N. Torrey Pines Rd. > La Jolla, CA 92037 > E-mail: fhong@salk.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > -- Fangxin Hong, Ph.D. Plant Biology Laboratory The Salk Institute 10010 N. Torrey Pines Rd. La Jolla, CA 92037 E-mail: fhong@salk.edu