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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?

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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.

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  • $\begingroup$ It is possible to update Seurat v2 objects to Seurat v3 objects via UpdateSeuratObject(). $\endgroup$
    – haci
    Mar 21 '20 at 10:23
  • $\begingroup$ I don’t know off hand, maybe give it a whirl and see. $\endgroup$
    – Devon Ryan
    Mar 21 '20 at 10:57

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