The introduction did a great job at motivating the need for this research but was overall too long. It would be better to spend less time on the high level details so you have more time for results.
Quality of presentation
Some plots/fonts were too small and hard to see. It's also not the best idea to include full tables from your code and best to summarize or annotate them to show important results.
Statistical analysis
The class sizes for Non-obese vs obese were quite imbalanced especially in Experiment 1.
What did the results look like after comBat? I would be curious to see the results for the merged databases.
Overall there was a lot of analysis done, I would have suggested to decrease the amount of databases you used for gene set enrichment or only show a few of the results due to time constraints.
Scientific maturity
Another way to decrease the scope of the project would be to narrow down your hypothesis to specific pathways that are known in literature.
Background/introduction
The introduction did a great job at motivating the need for this research but was overall too long. It would be better to spend less time on the high level details so you have more time for results.
Quality of presentation
Some plots/fonts were too small and hard to see. It's also not the best idea to include full tables from your code and best to summarize or annotate them to show important results.
Statistical analysis
The class sizes for Non-obese vs obese were quite imbalanced especially in Experiment 1.
What did the results look like after comBat? I would be curious to see the results for the merged databases.
Overall there was a lot of analysis done, I would have suggested to decrease the amount of databases you used for gene set enrichment or only show a few of the results due to time constraints.
Scientific maturity
Another way to decrease the scope of the project would be to narrow down your hypothesis to specific pathways that are known in literature.