How to get top 10 genes expressed in a cluster ( for cell type identification)?

Question

[Chris]

Hi all,

I try to label clusters but singleR result is not consistent with the marker gene for a cell type. Findmarker() or Findallmarker() seems could not get genes express in a cluster but they are used for comparison. Would you please suggest the function or code I should use in this case? I appreciate it!

[bk11]

These two functions- Findmarker() or Findallmarker() had been discussed before. Please check it out in the link below:-

FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat

[Chris]

Thank you for the information. I have read it before, very helpful. Unfortunately, I can't use it for this question.

Answer 1

[yhdist]

You want to find the genes with the highest expression or the highest rates of differential expression? Surely you can find the 10 "most epxressed" genes on your vst data before drawing your Heatmap, if you have any.

There can be a million reasons why your marker does not reflect your expectations depending on your process.

[Chris]

Just a modification that I want to find all genes expressed in a cluster. I think Findallmarker() will do that.

[yhdist]

The Seurat object already tells you what the clusters are, if that's what you want.

[Chris]

Thank you. Seurat object will tell the cluster number but not which genes or cell type of that cluster. I think I figured it out.

[yhdist]

It will tell you which cells are involved, but it won't be able to tell you the cell type unless you've already labeled them. I hope this worked out in the end.