You need to define
FindMarkers and cannot keep it as
Allowed idents are members of the named vector
Idents(seurat_obj). The names of this vector are cell names. Originally,
Idents(seurat_obj) holds cluster indices which lends itself to find markers between clusters.
However you can set
Idents(seurat_obj) to other variables.
An easy way to do this is by using one of the columns in the metadata matrix of seurat_obj (whose
rownames are also cell names). Check
head(email@example.com) to determine if you already have a column holding KO or WT per each row. Say this column name is stim. You can now redefine Idents as follows:
Idents(seurat_obj) <- seurat_obj$stim and continue with
FindMarkers(seurat_obj, ident.1="KO" ident.2="WT").
If you do not have a proper column in the metadata matrix, create a new one which holds KO/WT information (e.g.
seurat_obj$newColumn<-...) and then use this column to redefine
modified 5 weeks ago
5 weeks ago by
jomo018 • 610