Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-28T17:31:12.973Z
Answers.Text: 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?
Answers.UserDisplayName: hua
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-28T20:46:31.687Z
Answers.Text: You can set the `ident.use` parameter of `SetIdent()` function to one of the columns in your `meta.data` slot of your `Seurat` object.
Answers.UserDisplayName: haci
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-09-23T17:37:19.690Z
Answers.Text: 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().
Answers.UserDisplayName: swbarnes2
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-12-28T12:52:30.557Z
Answers.LastActivityDate: 2019-12-28T12:52:30.557Z
Answers.UserDisplayName: haci
Body: <p><a href="https://i.sstatic.net/rlI7l.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/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>
  
Tags: <seurat><single-cell>
Title: Finding differentially expressed genes between two samples
ThreadText: # Finding differentially expressed genes between two samples
  
  (Asked by: username_0 on 2019-12-25)
  
  [![enter image description here](https://i.sstatic.net/rlI7l.png)](https://i.sstatic.net/rlI7l.png)
  
  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.
  
  **Tags:** seurat, single-cell
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-12-28. Score: 1
  
  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.
  
  > **Comments:**
  > **username_0**: Hi username_1, 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?  
  > **username_1**: You can set the `ident.use` parameter of `SetIdent()` function to one of the columns in your `meta.data` slot of your `Seurat` object.  
  > **username_2**: 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().  
  
  ---
  
  