# Finding differentially expressed genes between two samples

Hi, I was wondering whether we can find the differentially expressed genes between the Double-KO and the Shox2-KO. For the FindMarker() function, only see the differential expressed gene between different identities. I don't know whether we can find the differential expressed gene between only these two samples.

If I understand your question correctly, you can simply use SetIdent() to change the "default identity" to your samples and then use FindMarker() with the ident.1 = "Double-KO" and ident.2 = "Shox2-KO".
• You can set the ident.use parameter of SetIdent() function to one of the columns in your meta.data slot of your Seurat object. – haci Dec 28 '19 at 20:46