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anndataR::from_Seurat error message update #203

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vmedaert opened this issue Nov 25, 2024 · 0 comments
Open

anndataR::from_Seurat error message update #203

vmedaert opened this issue Nov 25, 2024 · 0 comments

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@vmedaert
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I downloaded a seurat object from https://zenodo.org/record/3531889/files/seuratObj.rds

The following code

seuratObj <- SeuratObject::UpdateSeuratObject(readRDS("./data/rds/seuratObj3531889.rds"))
ann <- anndataR::from_Seurat(seuratObj, "HDF5AnnData")

gives the following error message despite the call to SeuratObject::UpdateSeuratObject

Error in anndataR::from_Seurat(seuratObj, "HDF5AnnData") : 
  Assay 'RNA' is not a valid Seurat v5 assay.
Please use `SeuratObject::UpdateSeuratObject()` to upgrade the object to Seurat v5.

the problem was solved by

seuratObj[["RNA"]] <- as(object = seuratObj[["RNA"]], Class = "Assay5")

Perhaps the error message could be updated with a mention to this class conversion?

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