Hi! I am trying to understand what is happening when I use AggregateExpression() in Seurat v5 for pseudobulk. This is my code

pseudobulk <- AggregateExpression(seurat_obj, assays = "RNA" , group.by = c("subtype", "DiseaseStage", 
                                                                           "DiseaseStage_subtype"), return.seurat = TRUE)
pseudobulk@meta.data <- as.data.frame(lapply(pseudobulk@meta.data, function(column) {
  column <- gsub("-", "_", column)
  column <- sub("^g", "", column)
  return(column)
}))


DEGs <- data.frame()

subtype_list <- sort(unique(seurat_obj@meta.data[["subtype"]]))

ident.1_list <- sort(unique(seurat_obj@meta.data[["DiseaseStage"]]))
ident.1_list <- ident.1_list[2:length(ident.1_list)] 

for (subtype in subtype_list){
  for (DiseaseStage in ident.1_list) {
    control_group <- paste0("WT", "__", subtype)
    disease_group <- paste0(DiseaseStage, "__", subtype)
    if (control_group %in% unique(pseudobulk@meta.data$DiseaseStage_subtype) &
        disease_group %in% unique(pseudobulk@meta.data$DiseaseStage_subtype)){

      Idents(pseudobulk) <- "DiseaseStage_subtype" 
      DiseaseStage_DEGs <- FindMarkers(pseudobulk, ident.1 = disease_group, ident.2 = control_group, verbose = FALSE,
                                   test.use = "wilcox", only.pos = FALSE, logfc.threshold = 0.5)
      DEGs <- rbind(DEGs, DiseaseStage_DEGs)
    }
  }
}

and I get

Error in `FindMarkers()`:
! Cells in one or both identity groups are not present in the data requested

which is odd because both

control_group %in% unique(pseudobulk@meta.data$DiseaseStage_subtype)

and

disease_group %in% unique(pseudobulk@meta.data$DiseaseStage_subtype)

return TRUE. Anyone has an explanation?