I have completed CuffDiff analysis on my transcriptomics data and I am currently trying to look at replicate variation within my treatment groups using my CuffNorm output. I have 6 treatment groups and each have either three or four replicates (different Day's). When I look at the CuffNorm output, the treatments have been assigned a label of either 1, 2, 3 or 4 (depending on the number of replicates), however I don't know which these correspond to (whether they correspond to my Day 1, Day 2 or Day 3 replicates). Is there any way to know this from the CuffNorm output?
Thanks!