Sorry for the basic question, but I've really confused myself. I've done a lot of reading, but I'm missing some of the basic understanding I need to properly understand most of the information I can find online.
I have some cells, and have treated them under 4 different conditions - 1 control condition and 3 experimental conditions.
I have a very long list of genes expressed under each condition, along with fold change (relative to the control cell gene expression)
To be honest, I'm lost at this point. What is the best way of comparing these lists?
Also, how would I go about doing GSEA on each list? Would I use the control gene expression as the 'comparator gene set' for the GSEA? Or should I look for available gene expression values for the organ the cells originate from - (my thinking is that this would not be a fair comparison for enrichment, as my cells only represent about 1% of the total organ cell count?)
Any help here would be very appreciated, I've spent days reading things I don't understand. Even a link to some good beginner friendly reading material would be great, thank you for reading my post
