I have two sets of data; 12 hours control and experiment and 48 hours control and experiment. I am only interested in known transcripts so I will be using cuffdiff directly. My question is how do I properly combine the controls and each time period as replicate groups in cuffdiff? Do I create a group for each time period and just add the control and experiment in batch mode, or do I add the control and experiment as individual replicates in each group?
In addition, If I have a sample with two replicates and a control with two replicates do I add both controls and both experimental replicates to individual groups?