Seurat define manually a cluster and find markers I am aware of this question Manually define clusters in Seurat and determine marker genes that is similar but I couldn't make tit work for my use case.
So I have a single cell experiments and the clustering id not great I have a small groups of 6 cells (I know it is extremely small, but nonetheless I would like to make the most of it) that are clearly isolate in UMAP and display marker that I am interresting in.
I managed to get those cells names in barcode (e.g.: AGCCAGCTCGCTTTAT).
I would like to compute differential expression of those cells against all others groups (using FindMarkers or FindAllMarkers).
I tried to manually define the cluster in:
Seurat_obj@meta.data$seurat_clusters
But using FindMarkers (it says this groups don't exist)
then I try to modify
s_19270BC@active.ident
but then it could not found metadata attached to my newly define group.
I am kind of stuck and any help is warmly welcome
Code
My R is quite rusty...
names_ # a vector with the names of the cell I want as a cluster

# my seurat object have 5 cluster 0..4. So I want to add a 6th clusters with id 5

#First attempt manually modify the vector active.ident and cluster
# they are both factor so we need to add a factor level
levels(seurat_obj@active.ident) = c(levels(seurat_obj@active.ident), 5)
levels(seurat_obj@meta.data$seurat_clusters) = c(levels(seurat_obj@meta.data$seurat_clusters), 5)
# then modify them :
seurat_obj@active.ident[which(row.names(seurat_obj@meta.data) %in%  names_)] = 5
seurat_obj@meta.data$seurat_clusters[which(row.names(seurat_obj@meta.data) %in%  names_)] = 5

FindMarkers(s_19270BC, ident.1 = 5)
 

So This morning it works... I don't know what I have done yesterday...
EDIT:
I added the Code I used
It would have been better if you have shared your code as well as the error messages you got format these as such.

As far as I can understand, your problem is that you failed to make your cluster as default ids. For this you can use:

seurat_obj &lt;- SetIdent(seurat_obj, id=seurat_obj@meta.data$column_of_interest).


The cluster identities are stored in the @meta.data slot of your object.