I have a simple experiment with 2 treatments (S and F) in a loop design. For each treatment I have 3 biological replicates (S1 to S3 and F1 to F3) and for each biological replicate there are 2 technical replicates (a and b). Biological reps are from different plants, while technical reps are different RNA extraction from the same plant. How do I deal with this in limmaGUI? Here is a layout of the design. Any help would be much appreciated. Array Cy3 Cy5 RF1 S1a F1a RF2 F1a S1b RF3 S1b F1b RF4 F1b S2a RF5 S2a F2a RF6 F2a S2b RF7 S2b F2b RF8 F2b S3a RF9 S3a F3a RF10 F3a S3b RF11 S3b F3b RF12 F3b S1a Cecilia McGregor PhD Student Louisiana State University Baton Rouge LA, 70803 USA