Question: Integrate four scRNA-seq datas
0
gravatar for 2962873004
7 weeks ago by
29628730040
29628730040 wrote:

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.
rna-seq • 192 views
ADD COMMENTlink modified 22 days ago by Biostar ♦♦ 20 • written 7 weeks ago by 29628730040
1
gravatar for rpolicastro
7 weeks ago by
rpolicastro1.7k
rpolicastro1.7k wrote:

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.

ADD COMMENTlink written 7 weeks ago by rpolicastro1.7k

But there's always a warning message after this step

ADD REPLYlink written 7 weeks ago by 29628730040

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

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by rpolicastro1.7k

Is this warning okay

> immune.combined <- IntegrateData(anchorset = immune.anchors, dims = 1:20)
Warning: Adding a command log without an assay associated with it
ADD REPLYlink modified 5 weeks ago by RamRS30k • written 7 weeks ago by 29628730040

Yea, that can be ignored.

ADD REPLYlink written 5 weeks ago by rpolicastro1.7k
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