Integrate four scRNA-seq datas

Question

[2962873004]

What do I do with this warning when I'm putting together the data?

immune.anchors <- FindIntegrationAnchors(object.list = list(HLJ1, HLJ2,HLJ3,HLJ4), dims = 1:20)

Warning message:
In CheckDuplicateCellNames(object.list = object.list) :
  Some cell names are duplicated across objects provided. Renaming to enforce unique cell names.

Answer 1

[rpolicastro]

You can ignore that. It's just saying there is some overlap in cell barcodes between samples, so it will add a suffix to the cell barcodes.

[2962873004]

But there's always a warning message after this step

[rpolicastro]

That's fine, there will almost always be matching cell barcodes since they are not completely randomly generated when 10X are synthesizing their beads.

[2962873004]

Is this warning okay

> immune.combined <- IntegrateData(anchorset = immune.anchors, dims = 1:20)
Warning: Adding a command log without an assay associated with it

[rpolicastro]

Yea, that can be ignored.