Hi, I have a question about using sam method in siggenes package. My R version is 1.9.0 and my siggenes package version is 1.0.6. I took a look at the usage page for sam and I'm a little confused about two arguments: data and cl since it is not really clear to me what their format should be. I have a file testdata.txt that contains 6 columns and each row contains intensity value. This data represent unpaired two class comparisons, each class has 3 replicates hence there are 6 columns. So in R I do scan data as follow: > data<-scan("testdata.txt") Then for cl argument, it is a vector containing the class labels of the samples. In this case I set the cl as follows: > cl<-c(0,0,0,1,1,1) This is to show that I have two classes for comparisons. Am I doing this wrong? Since I don't seem to find anything on this format on the internet at all. So I went ahead and execute sam as follows: > samdata<-sam(data,cl) Then I got the following error: Error in data[, c(x,y)] : incorrect number of dimensions. Any advice on this will be greatly appreciated. Thank you, Saran [[alternative HTML version deleted]]