[BioC] How to deal with technical replicates in limmaGUI?

[Cecilia McGregor]

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