How to deal with spatial data

[ElyasMo]

Hi,
Although you mentioned before #26, I would like to ask for more assistance regarding how to deal with spatial data.
Considering that the current version of scCATCH do not support spatial data, I tried to treat my data as a single cell data set:

## Transform Seurat object to SingleCellExperiment object
Idents(HE_control_2) <- HE_control_2$seurat_clusters
sce.HE_control_2 <- as.SingleCellExperiment(HE_control_2)

But again after trying to annotate my dataset I receive an error:

clu_markers <- findmarkergenes(sce.HE_control_2,
                               species = "Human",
                               cluster = 'All',
                               match_CellMatch = TRUE,
                               cancer = NULL,
                               tissue = "Brain",
                               cell_min_pct = 0.25,
                               logfc = 0.25,
                               pvalue = 0.05)

Error in findmarkergenes(sce.HE_control_2, species = "Human", cluster = "All",  : 
  trying to get slot "data" from an object of a basic class ("NULL") with no slots

Any ideas on how to make it work?
Thank you very much in advance.

[multitalk]

Hello, you don't need to transform Seurat object to SingleCellExperiment object. You just need to make sure the normalized data is stored in the Seurat object by checking sce.HE_control_2[['RNA']]@data

[ElyasMo]

Thank you for the response,
According to your guidance and as a complementary comment, I fixed the problem by following this procedure:

#Renaming the "SCT" assay to "RNA" which have normalized values in data slot.
HE_sample1_RNA <- RenameAssays(HE_sample_1, SCT="RNA")

#and next doing the annotation by scCATCH and it worked fine.