Hi Alessandro, > hi hiedi, > how are you? > > I 'd like to use HTqPCR to analyze our expression data. > > I have been given the following dataset (attached) that consists of 80 > samples and 48 targets. Each target has been measured twice so totally > there are 80 * 48 * 2 = 7680 measurements done in cards containing 48 > targets and 4 samples (so totally 20 cards). > > How would you shape this table in a format that might be read into HTqPCR? > There are (at least) 2 different ways of doing this. 1) Read your data into R using any standard function, such as read.table(). Create your qPCRset-object using new("qPCRset", ...) 2) Read your data into R using readCtData(). Re-format the object according to your data using readCtLayout. There are examples of both approaches in the vignette, section 13.6. Which one you prefer is a question of personal preference. The second may be useful when you have a lot of information in addition to your Ct values (such as feature classes, categories etc.), but that doesn't seem to be the case for your data. You can try one of these two, and if it doesn't seem to work, let me know. HTH \Heidi > thanks very much for your help! > Alessandro >