search

satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
Other
2.31k stars 919 forks source link

Can't follow the tutorial for Slide-Seq #9354

Open yingzhang121 opened 2 months ago

yingzhang121 commented 2 months ago

Hi, help,

I tried to follow the Slide-seq vignettes, but I got stuck at the very beginning. See the error below:

> slide.seq <- LoadData("ssHippo")
Validating object structure
Updating object slots
Ensuring keys are in the proper structure
Warning: Assay Spatial changing from Assay to Assay
Ensuring keys are in the proper structure
Ensuring feature names don't have underscores or pipes
Updating slots in Spatial
Updating slots in image
Validating object structure for Assay ‘Spatial’
Validating object structure for SlideSeq ‘image’
Object representation is consistent with the most current Seurat version
Error in as.vector(x) : no method for coercing this S4 class to a vector

Also, in the provided file of "mouse_hippocampus_reference.rds", all the gene names are uppercases, which definitely breaks the naming convention of mouse genes which are just capitalized.

I am using Seurat v5.1.0 in R v4.4.0.

zskylarli commented 1 month ago

Hi - I am unable to reproduce your issue; can you list your sessionInfo() including for SeuratObject, SeuratData, and ssHippo.SeuratData specifically? Thanks!