<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>

CC BY-SA 4.0
2019-12-28T17:31:12.973Z
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?
hua
CC BY-SA 4.0
2019-12-28T20:46:31.687Z
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
CC BY-SA 4.0
2020-09-23T17:37:19.690Z
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().
swbarnes2
CC BY-SA 4.0
2019-12-28T12:52:30.557Z
2019-12-28T12:52:30.557Z
haci
<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>

<seurat><single-cell>
Finding differentially expressed genes between two samples
# 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

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## 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 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?  
> **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().  

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