Open eblchen opened 1 month ago
Can you post the output of traceback()
after receiving the error?
Best, Sam
Sure, thanks for helping with this!
> entry.seurat <- Merge_Seurat_List(entry.list)
Error in names(model.list) <- all.levels :
attempt to set an attribute on NULL
> traceback()
8: merge.SCTAssay(x = objects[[idx.x]][[assay]], y = lapply(X = objects[idx.y],
FUN = "[[", assay), labels = projects, add.cell.ids = NULL,
collapse = collapse, merge.data = merge.data)
7: merge(x = objects[[idx.x]][[assay]], y = lapply(X = objects[idx.y],
FUN = "[[", assay), labels = projects, add.cell.ids = NULL,
collapse = collapse, merge.data = merge.data)
6: merge.Seurat(x = x, y = y, merge.data = merge.data, project = project)
5: merge(x = x, y = y, merge.data = merge.data, project = project)
4: fn(out, elt, ...)
3: reduce_impl(.x, .f, ..., .init = .init, .dir = .dir)
2: reduce(list_seurat, function(x, y) {
merge(x = x, y = y, merge.data = merge.data, project = project)
})
1: Merge_Seurat_List(entry.list)
>
ok thanks.
What happens if you run:
merged <- merge(entry.list[[1]], entry.list[[2:length(x = entry.list)]])
Best, Sam
Hi,
Just following up on my message from last week.
Best, Sam
Hi Sam, Sorry it's taken a while to reply have been away! This was the result:
> merged <- merge(entry.list[[1]], entry.list[[2:length(x = entry.list)]])
Error in (function (cond) :
error in evaluating the argument 'y' in selecting a method for function 'merge': subscript out of bounds
no worries! Sorry this was my bad on previous code. Try running this (removed bracket):
merged <- merge(entry.list[[1]], entry.list[2:length(x = entry.list)])
Best, Sam
Hi @eblchen,
No worries if you haven't had time but just following up on my previous post.
Best, Sam
Hi Sam, Sorry only just got back from travelling!
> merged <- merge(entry.list[[1]], entry.list[2:length(x = entry.list)])
Error in names(model.list) <- all.levels :
attempt to set an attribute on NULL
This was the error. Thanks for your help with this!
Hi @eblchen,
So sorry I've been in and out as well. So this tells me that the issue is coming from Seurat objects and not scCustomize. How many objects are in your list?
Best, Sam
Cannot merge Seurat object list get the following error:
Any pointers would be appreciated :)