Hello Ferdinando, sorry for the delay in getting back to you. Questions about bioconductor packages are usually best asked at the bioconductor email list (mentioned in the HTqPCR vignette and cc'd here), that way you get a better chance of an answer in case the developer is currently unavailable. HTqPCR should be able to handle files containing data from multiple runs, although I have only tested this with SDS files, not SDS2.2. In the readCtData there is a parameter n.data, which indicates the number of data sets present in each file. So if you have for example a file with results from 8 cards, you should be able to say something like: qset <- readCtData(files="data.txt", n.features = 384, SDS = TRUE, n.data = 8) This will read in 8*384 lines of data from the file after the header, and split them into the 8 individual runs. Likewise, if you've got multiple input files, one with 8 and one with 6 runs you can combined them with: qset <- readCtData(files=c("data.txt", "data2.txt"), n.features = 384, SDS = TRUE, n.data = c(8,6)) If this doesn't work, then please send me the exact commands that you used and the error message you got from R. If the SDS header has changed I might need to update HTqPCR accordingly. HTH \Heidi On 14 Oct 2010, at 15:47, Ferdinando Pucci wrote: > Dear Dr. Heidi, > > I am trying to use HTqPCR, I think it may really improve my > productivity. > > This is to report some difficulties with the very first step, data > import. I am not new to R, and I have SDS2.2 exported file. It > seems that I should have a separate file for each sample, but > usually you have a .sdm file with all the runs. When you export the > Cts from this .sdm file you get a single txt file. > > So, what should I do to import my data from this single txt file > containing all my samples? > > Thank you! > Ferdinando [[alternative HTML version deleted]]