2
$\begingroup$

enter image description here

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.

$\endgroup$
0
$\begingroup$

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.

$\endgroup$
3
  • $\begingroup$ Hi haci, that is a good idea. But I have tried to look the script of SetIdent(), find some difficulties to do it. Can you please give me more detail? $\endgroup$ – hua Dec 28 '19 at 17:31
  • $\begingroup$ You can set the ident.use parameter of SetIdent() function to one of the columns in your meta.data slot of your Seurat object. $\endgroup$ – haci Dec 28 '19 at 20:46
  • $\begingroup$ I'm not sure this is right. SetIdent is used to assign new ident information; you give it a vector of cells to tag. All you want to do is change the active ident that FindMarkers will use, and you do that with Ident(). $\endgroup$ – swbarnes2 Sep 23 '20 at 17:37

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.