<p><code>Seurat</code> is expecting individual datasets to be normalized separately prior to data integration. In that respect lists of objects corresponding to different datasets are handy to manipulate each object/dataset individually.</p>

<p>In your case you do not need to do any splitting, you have an object corresponding to each of your datasets.</p>

<p>If you would have started with a single count matrix of all datasets then you would need to split your data based on batches/experimental condition/...</p>

CC BY-SA 4.0
2019-09-23T07:53:00.440Z
2019-09-23T07:53:00.440Z
haci
<p>I want to do comparative analyses of my two individual single cell RNA-Seq datasets in Seurat. And I load and list my data as follows:</p>

<pre><code>Control.data &lt;- Read10X("~/Documents/...  Control_filtered_feature_bc_matrix")

Control &lt;- CreateSeuratObject(counts  = Control.data, project = "Control_summary", min.cells = 3, min.features = 200)

Mut.data &lt;- Read10X("~/Documents/... /Mut_filtered_feature_bc_matrix")

Mut &lt;- CreateSeuratObject(counts  = Mut.data, project = "Mut_summary", min.cells = 3, min.features = 200)

Object&lt;- list(Control,Mut)

names(Object) &lt;- colnames(Object)
</code></pre>

<p>Then the protocol <a href="https://satijalab.org/seurat/v3.1/immune_alignment.html" rel="nofollow noreferrer">https://satijalab.org/seurat/v3.1/immune_alignment.html</a> said, I need to use <code>SplitObject</code> function, but what do I split by?</p>

<pre><code>Object_list &lt;- SplitObject(Object, split.by = "?")
</code></pre>

CC BY-SA 4.0
2019-09-23T06:55:16.933Z
Can you please edit your post so as to include the link for the protocol that you have mentioned? Moreover, you have formatted your code as a "quote", please also change this to "code".
haci
<r><scrnaseq>
How to load and split my two individual datasets when integrating datasets in Seurat?
# How to load and split my two individual datasets when integrating datasets in Seurat?

(Asked by: username_0 on 2019-09-23)

I want to do comparative analyses of my two individual single cell RNA-Seq datasets in Seurat. And I load and list my data as follows:
Control.data <- Read10X("~/Documents/...  Control_filtered_feature_bc_matrix")

Control <- CreateSeuratObject(counts  = Control.data, project = "Control_summary", min.cells = 3, min.features = 200)

Mut.data <- Read10X("~/Documents/... /Mut_filtered_feature_bc_matrix")

Mut <- CreateSeuratObject(counts  = Mut.data, project = "Mut_summary", min.cells = 3, min.features = 200)

Object<- list(Control,Mut)

names(Object) <- colnames(Object)

Then the protocol https://satijalab.org/seurat/v3.1/immune_alignment.html said, I need to use SplitObject function, but what do I split by?
Object_list <- SplitObject(Object, split.by = "?")

**Tags:** r, scrnaseq
> **Comments:**
> **username_1**: Can you please edit your post so as to include the link for the protocol that you have mentioned? Moreover, you have formatted your code as a "quote", please also change this to "code".  

---

## 1 answers

### Answer by username_1 on 2019-09-23. Score: 4

`Seurat` is expecting individual datasets to be normalized separately prior to data integration. In that respect lists of objects corresponding to different datasets are handy to manipulate each object/dataset individually.

In your case you do not need to do any splitting, you have an object corresponding to each of your datasets.

If you would have started with a single count matrix of all datasets then you would need to split your data based on batches/experimental condition/...


---

