MarcElosua/SPOTlight

assay %in% SeuratObject：：Assays（x） is not TRUE

628511miao opened this issue · 2 comments

628511miao commented

I am performing SPOTlight and I am getting this error:
#res <- SPOTlight(

  • x = sce1,
  • y = stRNA,
  • groups = sce$t_group,
  • mgs = mgs_df,
  • hvg = hvg,
  • weight_id = "mean.AUC",
  • group_id = "cluster",
  • gene_id = "gene")
    Error in .extract_counts(y, assay, slot) :
    assay %in% SeuratObject::Assays(x) is not TRUE
axiba053 commented

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