Error Merge

[eblchen]

Cannot merge Seurat object list get the following error:

entry.seurat <- Merge_Seurat_List(entry.list)
Error in names(model.list) <- all.levels : 
  attempt to set an attribute on NULL

Any pointers would be appreciated :)

[samuel-marsh]

Can you post the output of traceback() after receiving the error?

Best, Sam

[eblchen]

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)
> 

[samuel-marsh]

ok thanks.

What happens if you run:

merged <- merge(entry.list[[1]], entry.list[[2:length(x = entry.list)]])

Best, Sam

[samuel-marsh]

Hi,

Just following up on my message from last week.

Best, Sam

[eblchen]

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

[samuel-marsh]

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

[samuel-marsh]

Hi @eblchen,

No worries if you haven't had time but just following up on my previous post.

Best, Sam

[eblchen]

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!

[samuel-marsh]

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

[samuel-marsh]

Hi @eblchen

Just checking in to see if this is still an issue or if I can close the issue?

Thanks!! Sam

[eblchen]

Hi Sam, Don’t think I solved it but found a workaround for now so happy to close the ticket sorry for not getting back to you sooner and thank you for all your help! Best wishes, Emilia

Emilia Chen | PhD Student

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From: Samuel Marsh @.> Sent: Thursday, August 22, 2024 1:21 PM To: samuel-marsh/scCustomize @.> Cc: Emilia Chen @.>; Mention @.> Subject: Re: [samuel-marsh/scCustomize] Error Merge (Issue #187)

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Hi @eblchenhttps://github.com/eblchen

Just checking in to see if this is still an issue or if I can close the issue?

Thanks!! Sam

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