Seurat Assay5

[ValYianni]

Package no longer works if you upgrade to the new version of Seurat.

Error in ncol(df) : 
  no slot of name "meta.features" for this object of class "Assay5"
In addition: Warning message:

[Junedays]

SAME ISSUE

[haukeh90]

Hi,

this problem can be circumvented by converting the V5 to a V3 assay in the seurat object before using sceasy:

Leukocytes[["RNA3"]] <- as(object = Leukocytes[["RNA"]], Class = "Assay")
DefaultAssay(Leukocytes) <- "RNA3"
Leukocytes[["RNA"]] <- NULL
Leukocytes <- RenameAssays(object = Leukocytes, RNA3 = 'RNA')

please find additional information here: https://satijalab.org/seurat/articles/seurat5_essential_commands

Best

Hauke

[august-li-alt]

Hi,

this problem can be circumvented by converting the V5 to a V3 assay in the seurat object before using sceasy:

Leukocytes[["RNA3"]] <- as(object = Leukocytes[["RNA"]], Class = "Assay") DefaultAssay(Leukocytes) <- "RNA3" Leukocytes[["RNA"]] <- NULL Leukocytes <- RenameAssays(object = Leukocytes, RNA3 = 'RNA')

please find additional information here: https://satijalab.org/seurat/articles/seurat5_essential_commands

Best

Hauke

Thank you very much. Your answer helped me a lot

[luzzhou]

Hi,

this problem can be circumvented by converting the V5 to a V3 assay in the seurat object before using sceasy:

Leukocytes[["RNA3"]] <- as(object = Leukocytes[["RNA"]], Class = "Assay") DefaultAssay(Leukocytes) <- "RNA3" Leukocytes[["RNA"]] <- NULL Leukocytes <- RenameAssays(object = Leukocytes, RNA3 = 'RNA')

please find additional information here: https://satijalab.org/seurat/articles/seurat5_essential_commands

Best

Hauke

Hi @haukeh90. thank you for your sharing. But I encountered another problem in the process: obj[["RNA3"]] <- as(object = obj[["RNA"]], Class = "Assay")
Warning: No layers found matching search pattern provided
Warning: No layers found matching search pattern provided
Warning: No layers found matching search pattern provided
Warning: No layers found matching search pattern provided
Warning: No layers found matching search pattern provided
Error in .subset2(x, i, exact = exact) : subscript out of bounds
In addition: Warning messages:
1: Layer ‘data’ is empty
2: Layer ‘scale.data’ is empty.

R version 4.4.0 (2024-04-24)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] sceasy_0.0.7 reticulate_1.36.1 dplyr_1.1.4 SeuratData_0.2.2
[5] Seurat_5.0.3 SeuratObject_5.0.2 sp_2.1-4

If anyone has a solution, I would be very grateful

[JAMKuttan]

@luzzhou I am having the same issue suddenly as of last week. Any luck?