ERROR

[haitianyisee]

你好 我在用示例数据进行的时候出现了以下错误
brain_traint <- CellTrek::traint(st_data=brain_st_cortex, sc_data=brain_sc, sc_assay='RNA', cell_names='cell_type')
Finding transfer anchors...
Using 2000 features for integration...
Running CCA
Merging objects
Finding neighborhoods
Finding anchors
Found 3730 anchors
Data transfering...
Finding integration vectors
Finding integration vector weights
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Transfering 2000 features onto reference data
Creating new Seurat object...
Warning: Data is of class data.frame. Coercing to dgCMatrix.
Error in CellTrek::traint(st_data = brain_st_cortex, sc_data = brain_sc, :
no slot of name "counts" for this object of class "Assay5"
In addition: Warning messages:
1: Command ScaleData.RNA changing from SeuratCommand to SeuratCommand
2: Adding image data that isn't associated with any assays

请问是某些R包的版本问题吗

[tsoruu]

Hi @haitianyisee, I have similar problem with R version 4.3.2 with Seurat v5.0.1 from CRAN repository. This would be my guess, but I think you're using version 5 of Seurat too, judging from the "Assay5" error? I've read some discussion that downgrading the Seurat to version 3 would help in this error. I've also open an issue similar to this link