Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic / sctransform

[pstrangw]

Hi,

When attempting to run sctransform in R I receive the following error:

Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic

Please could you help me troubleshoot this issue.

merged.seurat.object <- Seurat::SCTransform(merged.seurat.object)

This is a merged Seurat object composed of 10 layers.

Thanks for your help.

Best,
Patrick

[pstrangw]

A quick update to this. I can perform sctransform on the merged seurat object without issue if there is only 1 layer present. If the object is split into 10 layers based on 'Sample' identifier in the meta data then I receive the above error. Code below re joining layers and splitting object into layers.

#join layers
merged.seurat.object<- JoinLayers(merged.seurat.object,  assay = "RNA")

#split into 10 layers based on Sample identifier in metadata
merged.seurat.object[["RNA"]] <- split(merged.seurat.object[["RNA"]], f = merged.seurat.object$Sample)

Is there a useful way I can share the merged.seurat.object.RDS file? It is too large even zipped to attach here.

[saketkc]

You can email them to me at schoudhary@nygenome.org

[pstrangw]

Thanks Saket - I have emailed you the merged seurat file.