I have RNA-seq data from the following two experiments:
- Onion grown under four different conditions (control, 1, 2, 3), of which three biological replicates were taken from each condition 72 hours after inoculation.
- Onion grown under condition 2 over the course of 96 hours, with a sample taken at 10 time-points (including 72 hours). However, only two replicates were taken at 24 hours - no other replicates were taken throughout the experiment.
I understand that experiment 1 is fine, but that I won't be able to draw any reliable results from experiment 2 due to the lack of replicates. My plan is to base my research on the first experiment, but is there anything useful I can do with the data from the second? Could I use the second experiment to explore how expression levels of interesting genes identified in ex.1 change over time? It wouldn't form a significant part of the research, but it could help inform future work/form a hypothesis? What be the best way to visualise this? Use GFOLD? Could dispersion estimates from ex.1 be used in ex.2 to act as a proxy for the true dispersion?