text: user3171: 
  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.
  
  user3541: 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".
  Alternatively, you can "collapse" or "summarize" your single cell data into a pseudo-bulk and then use one of the bulk RNA-seq packages.
  
original_text: 3171: <p><a href="https://i.stack.imgur.com/rlI7l.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/rlI7l.png" alt="enter image description here"></a></p>
  
  <p>Hi, I was wondering whether we can find the differentially expressed genes between the <code>Double-KO</code> and the <code>Shox2-KO</code>. For the <code>FindMarker()</code> 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.</p>
   3541: <p>If I understand your question correctly, you can simply use <code>SetIdent()</code> to change the "default identity" to your samples and then use <code>FindMarker()</code> with the <code>ident.1 = "Double-KO"</code> and <code>ident.2 = "Shox2-KO"</code>.</p>
  
  <p>Alternatively, you can "collapse" or "summarize" your single cell data into a pseudo-bulk and then use one of the bulk RNA-seq packages.</p>
  