hello R-users, I'm trying to do time series analysis using the samr package. I have an excel sheet with 25 columns and 22811 lines. the first row has the names of the experiments and the first column contains the names of the genes. I saved this file to a tab-delimited table and tried to read it with read.table/read.delim with and without the header. >test_TS <- read.table("test_data_TS.txt" ) #constructing the vector >y=paste(c(rep(1,12),rep(2,12)),"Time",rep(c(1,24,3,48,6,9),2),sep="") >start=c(1,7,13,19) >for(i in start){ >y[i]=paste(y[i],"Start",sep="")} >for(i in start+5){ >y[i]=paste(y[i],"End",sep="")} >#p by n matrix of features, one observation per column >TS_group <- bind(test_TS[,2],test_TS[,4],test_TS[,6],test_TS[,8], test_TS[,10],test_TS[,12],test_TS[,3],test_TS[,5],test_TS[,7],test_TS[ ,9], test_TS[,11],test_TS[,13],test_TS[,14],test_TS[,16],test_TS[,18],test_ TS[,20], test_TS[,22],test_TS[,24],test_TS[,15],test_TS[,17],test_TS[,19],test_ TS[,23],test_TS[,25]) >gene_names <- test_TS[,1] >#data object für die samr Analyse >data_test=list(x=TS_group,y=y, logged2=TRUE) >#running samr analysis using the "slope" method >samr.obj_slope<- samr(data_test, resp.type="Two class unpaired timecourse", nperms=100, time.summary.type="slope") I'm getting an error message which I don't understand: 123456789101112131415161718192021222324Error in t(x[, jj, drop = F]) : (subscript) logical subscript too long I thought the problem was due to the fact that samr needs a matrix to work with, so I tries to convert the data frame to a matrix both using the data.matrix option >matrix_test_TS <- data.matrix(test_TS) and the scan option: > matrix_test_TS <- matrix(scan(test_TS)) after changing the frame to a matrix with data.matrix i'm getting the same error. Using scan I can't even read the file: Warning message: In scan(file, what, nmax, sep, dec, quote, skip, nlines, na.strings, : number of items read is not a multiple of the number of columns It would be very nice if someone can give me some hints about how to convert a data.frame object to a matrix (if it's necessary at all) and how to run a samr analysis using the command line and not the excel plugin! Thank you very very much in advance Assa -- Assa Yeroslaviz Kockelsberg 22 51371 Leverkusen [[alternative HTML version deleted]]