单细胞IntegrateLayers报错（自备）

在进行去批次时报错

#CCA
seurat_merge_v5 <- IntegrateLayers(
  object = seurat_pca, method = CCAIntegration,
  orig.reduction = "pca", new.reduction = "cca",
  verbose = FALSE
)


#报错
Error in UseMethod(generic = "Assays", object = object) : 
  no applicable method for 'Assays' applied to an object of class "NULL"

Error in UseMethod(generic = "Assays", object = object) : 
  no applicable method for 'Assays' applied to an object of class "NULL"

#harmony
seurat_merge_v5 <- IntegrateLayers(
  object = seurat_merge_v5, method = HarmonyIntegration,
  orig.reduction = "pca", new.reduction = "harmony",
  verbose = FALSE
)

报错：
Error in names(groups) <- "group" : attempt to set an attribute on NULL

解决：

IntegrateLayers: Error in UseMethod(generic = "Assays", object = object) : no applicable method for 'Assays' applied to an object of class "NULL" · satijalab/seurat · Discussion #9045 (github.com)

Hello, you likely haven't split your layers before running IntegrateLayers.

This line, above the section in the tutorial you have linked, is absolutely crucial :

ifnb[["RNA"]] <- split(ifnb[["RNA"]], f = ifnb$stim)

This replaces the SplitObject function in Seurat v4 integration pipeline. Here the f parameter needs to be one of the metadata column, it could be orig.ident, condition, treatment etc