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Newly Introduced Warning #13

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bbimber opened this issue May 10, 2021 · 2 comments · Fixed by #32
Closed

Newly Introduced Warning #13

bbimber opened this issue May 10, 2021 · 2 comments · Fixed by #32

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@bbimber
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bbimber commented May 10, 2021

Hello,

I assume this might be due to an updated seurat version, but our code just started spitting out this warning:

2021-05-10T06:32:14.3076028Z 11. Seurat:::PseudobulkExpression(...)
2021-05-10T06:32:14.3076758Z 13. SeuratObject:::CreateSeuratObject.default(...)
2021-05-10T06:32:14.3077559Z 14. SeuratObject::CreateAssayObject(...)
2021-05-10T06:32:14.3078195Z 16. SeuratObject:::as.sparse.matrix(x = counts, ...)
2021-05-10T06:32:14.3078760Z 17. SeuratObject:::CheckDots(...)

From what I can see, this is b/c as.sparse.Matrix is called here, with "...":

https://github.com/mojaveazure/seurat-object/blob/6d847461cb4993335e3467be85f59302ce01c4ce/R/assay.R#L130

and yet here it's called with the argument row.names:

https://github.com/mojaveazure/seurat-object/blob/6d847461cb4993335e3467be85f59302ce01c4ce/R/seurat.R#L958

should it?

@bbimber
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bbimber commented May 10, 2021

Also, I am using SeuratObject and Seurat 4.0.1

@timoast
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timoast commented Nov 23, 2021

This should be fixed by #32

@mojaveazure mojaveazure linked a pull request Nov 23, 2021 that will close this issue
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3 participants