Not sure if it is appropriate to ask so if it is not, please cancel the post!
Briefly I have to integrated 2 scRNA-seq datasets (damage vs damage+treatment) which are so similar that I could not see much differences between them (e.g., I get max 100 DEGs). I believe this is because of the nature of the dataset. However experimentally my colleagues observed differences between the same 2 conditions but when I look at the distribution of the DEGs. How do you think I should proceed? What would be the best practice?
Not sure if it is appropriate post! apologies if it is no!