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 = "?")
  • $\begingroup$ 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". $\endgroup$
    – haci
    Sep 23, 2019 at 6:55

1 Answer 1


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/...


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