I have tried to export the monocle data into Seurat and got the error

"Error in Seurat::CreateSeuratObject(raw.data = data, normalization.method = "LogNormalize",  :
  unused arguments (raw.data = data, normalization.method = "LogNormalize", do.scale = TRUE, do.center = TRUE, is.expr = monocle_cds@lowerDetectionLimit)
Calls: exportCDS
In addition: Warning message:
In if (export_to == "Seurat") { :
  the condition has length > 1 and only the first element will be used"

Here is my code seurat_SAN_cds_subset <- exportCDS(SAN_cds_subset)

Is anyone familiar with this?


There's no default for the export_to option, so you just need to specify export_to="Seurat". Note that monocle2 doesn't seem to be compatible with the newest Seurat (3.1) releases.

|improve this answer|||||
  • $\begingroup$ It is possible to update Seurat v2 objects to Seurat v3 objects via UpdateSeuratObject(). $\endgroup$ – haci Mar 21 at 10:23
  • $\begingroup$ I don’t know off hand, maybe give it a whirl and see. $\endgroup$ – Devon Ryan Mar 21 at 10:57

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.