I would like to run DEG analysis on cells within a set of clusters that are positive for my marker vs cells that are negative for my marker.
The clusters in question are 0, 1, 2, 3, 4, 6, 7, 8, 9 ,11, 12, and 13, and are all keratinocytes. I have renamed the idents of these clusters to 'keratinocytes'. I next looked for expression of my marker within the keratinocyte clusters, and then subset the cells into a 'marker-positive' group and a 'marker-negative' group. I understand that if I subset the keratinocytes, I will then be left with 2 seurat objects. How would I then perform DE between the 2 objects? Is there a better way to do this?
I would also like to know how would you strategise what cells are 'marker-positive' and what cells are 'marker-negative'? Would it be any cells that are > than the average expression can be classed as positive?
Thank you in advance!