Closed felixm3 closed 1 year ago
This is due to a missing key in the ATAC object stored in SeuratData. @mojaveazure maybe we can update this?
In the meantime, it can be fixed by running UpdateSeuratObject()
:
pbmc.atac <- UpdateSeuratObject(pbmc.atac)
pbmcMultiome has been updated in SeuratData - please make sure to first remove the dataset before installing the updated object
RemoveData("pbmcMultiome")
InstallData("pbmcMultiome")
This works now.
Thanks!
I got the same error mentioned in the issue title when I ran SCTransform
on a S4 and a S3 Seurat subject. But luckily, running UpdateSeuratObject
as @timoast commented before running SCTransform
fixed the error.
This is due to a missing key in the ATAC object stored in SeuratData. @mojaveazure maybe we can update this?
In the meantime, it can be fixed by running
UpdateSeuratObject()
:pbmc.atac <- UpdateSeuratObject(pbmc.atac)
Hello,
I’m trying to run the vignette “Integrating scRNA-seq and scATAC-seq data” https://satijalab.org/seurat/articles/atacseq_integration_vignette.html
I’m able to load both modalities.
However, when I run the next two lines:
The
pbcm.rna
line runs fine but thepbmc.atac
line has the error:The traceback is:
Minimal Reproducible example
Operating system: macOS Monterey v12.6.1
Output of
sessionInfo()