Dear Saran, When you use scan("testdata.txt"), the data is not read in as a matrix. It is read in as a vector. Try class(data) or length(data) to see. You will need to convert the vector into a matrix. t.data<-matrix(scan("testdata.txt"), byrow=TRUE, ncol=6) Alternative try using t.data<-read.table("testdata.txt", row.names=1, header=T) # assuming gene/array labels in first col and row check this using dim(t.data) and class(t.data). The number of col, ncol(data) should equal the length(cl). Hope this helps, Aedin 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) So I went ahead and execute sam as follows: 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.