2
$\begingroup$

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 = "?")
$\endgroup$
  • $\begingroup$ 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 at 6:55
4
$\begingroup$

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/...

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.