"The slot argument of SetAssayData() is deprecated as of SeuratObject 5.0.0. Please use the layer argument instead.

[Stephaniewy]

Warning message:
"The slot argument of SetAssayData() is deprecated as of SeuratObject 5.0.0.
i Please use the layer argument instead.
i The deprecated feature was likely used in the Seurat package.
Please report the issue at <https://github.com/satijalab/seurat/issues>."

but I'm not sure how I can deal with it.

Thanks in advance!

[YoukaiFromAccounting]

Hello @Stephaniewy; thank you for your message. The Seurat team is aware of this issue and are actively transitioning some core functions to use layer arguments rather than slot arguments; notably those used in GetAssayData(), SetAssayData(), and FetchData(). We should have a fix for this very soon!

[DanielBirtles]

Hello hope you are well!

I am receiving a similar message when trying to follow the 10x Visium Vignette at the point of data pre-processing:

"Error in FetchData():
! None of the requested variables were found: nCountSpatial
Run rlang::last_trace() to see where the error occurred.
Warning message:
The slot argument of FetchData() is deprecated as of SeuratObject 5.0.0.
ℹ Please use the layer argument instead.
ℹ The deprecated feature was likely used in the Seurat package.
Please report the issue at https://github.com/satijalab/seurat/issues."

Any advice on how to solve this?

Apologies if a basic question! I'm new to transcriptomic data analysis!

Best,

Daniel

[YoukaiFromAccounting]

Hello @DanielBirtles; thank you for your message. The missing requested variables issue was an unexpected result from the transition from Visium V1 to V2 objects from 10x Genomics (the new dataset used in the vignette is now Visium V2). As such, trying to subset based on imagerow and imagecol variables in the preprocessing steps doesn't work (since those variables don't exist anymore in V2 objects). We are currently editting the vignette with updated instructions for subsetting such to avoid that error.

Thank you for your continued interest in the Seurat project!

[DanielBirtles]

Thank you so much! I look forward to the updated vignette and appreciate the swift response! :)

[YoukaiFromAccounting]

The issue has just been fixed and the Spatial Vignette instructions on the Seurat website have been updated to ensure proper retrieval of spatial data image coordinates. Please let us know if there are any issues!

[Stephaniewy]

Thank you so much!