Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-09-23T07:53:00.440Z
Answers.LastActivityDate: 2019-09-23T07:53:00.440Z
Answers.UserDisplayName: haci
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-09-23T06:55:16.933Z
Comments.Text: 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".
Comments.UserDisplayName: haci
Tags: <r><scrnaseq>
Title: How to load and split my two individual datasets when integrating datasets in Seurat?
ThreadText: # 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/...
  
  
  ---
  
  