text: user6252: 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 = "?")
  
  
  user3541: 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/...
  
original_text: 6252: <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>
   3541: <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>
  