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I am performing SPOTlight and I am getting this error: #res <- SPOTlight(
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This is the software version, data structure, running code and error message. What is the cause? How to solve it? Thank you very much!
> packageVersion('SPOTlight') [1] ‘1.7.2’ > packageVersion('Seurat') [1] ‘4.3.0’ > sce class: SingleCellExperiment dim: 18975 40 metadata(0): assays(2): counts logcounts rownames(18975): A1BG A1BG-AS1 ... ZYG11A bP-21264C1.2 rowData names(0): colnames(40): SMC01-T_SMC01.T_CTGTGCTTCAGATAAG SMC01-T_SMC01.T_TAGCCGGCACGTCAGC ... SMC01-N_SMC01.N_CCATGTCTCACCTCGT SMC01-N_SMC01.N_TCATTACCATCTCCCA colData names(10): orig.ident nCount_RNA ... sizeFactor label reducedDimNames(0): mainExpName: RNA altExpNames(1): integrated > spdata An object of class Seurat 36122 features across 7347 samples within 2 assays Active assay: SCT (18037 features, 3000 variable features) 1 other assay present: Spatial 2 dimensional reductions calculated: pca, umap 1 image present: slice1 > res <- SPOTlight( x = sce, y = spdata, groups = colLabels(sce), mgs = mgs_df, hvg = hvg, weight_id = "mean.AUC", group_id = "cluster", gene_id = "gene",assay="SCT") Error in .extract_counts(y, assay, slot) : assay %in% SeuratObject::Assays(x) is not TRUE
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I am performing SPOTlight and I am getting this error:
#res <- SPOTlight(
Error in .extract_counts(y, assay, slot) :
assay %in% SeuratObject::Assays(x) is not TRUE
The text was updated successfully, but these errors were encountered: