Closed katimbach closed 3 months ago
Based on this: https://stackoverflow.com/questions/77487154/invalid-class-graph-object-superclass-mmatrix-not-defined-seurat-r it seems that this is an issue with the Matrix version with older Seurat versions. I downgraded to r-matrix from 1.6_5 to 1.6_1.1 in my environment and now it runs without issue.
That being said, I really recommend specifying the correct versions of Seurat/SeuratObject packages and the Matrix dependency in the recipe to build r-beyondcell, because currently with the default install it is unusable.
I'm trying to run the pipeline with a spatial sample. I was having issues with bcUMAP without specifying any PCs, but after downgrading Seurat and SeuratObject versions to v4 it worked and generated an elbow plot, see below:
However, now when I try to specify 10 PCs to run, I get the following error:
Here is my sessionInfo: