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Reprex:
obj <- LoadData("pbmcsca") obj[["RNA"]] <- split(obj[["RNA"]], f = obj$orig.ident) options(future.globals.maxSize = 3e+09) obj <- SCTransform(obj) obj <- RunPCA(obj, npcs = 30, verbose = F) obj <- IntegrateLayers( object = obj, method = RPCAIntegration, normalization.method = "SCT", verbose = F ) obj <- FindNeighbors(obj, dims = 1:30, reduction = "integrated.dr") obj <- RunUMAP(obj, dims = 1:30, return.model = T)
If we check the obj structure, we will see that the IntegrateLayers function didn't add the 'integrated' assay to obj, which is already alarming:
obj
IntegrateLayers
> obj An object of class Seurat 56793 features across 31021 samples within 2 assays Active assay: SCT (23099 features, 3000 variable features) 3 layers present: counts, data, scale.data 1 other assay present: RNA 3 dimensional reductions calculated: pca, integrated.dr, umap
Instead, the SCT slot contains two SCTmodel(s), and I don't know how to join them, to be honest.
> obj@assays$SCT SCTAssay data with 23099 features for 31021 cells, and 2 SCTModel(s) Top 10 variable features: LYZ, S100A8, S100A9, IGKC, RP11-1143G9.4, CH507-513H4.3, IGLC2, PPBP, GNLY, IGLC3
The problem arises when we want to generate Azimuth reference from this integrated object:
obj_Azimuth <- AzimuthReference( + object = obj, + refUMAP = "umap", + refDR = "pca", + refAssay = "SCT", + metadata = 'CellType', + dims = 1:50, + k.param = 31, + reference.version = "1.0.0" + ) Error in AzimuthReference(object = obj, refUMAP = "umap", refDR = "pca", : refAssay (SCT) should contain a single SCT model. In addition: Warning message: CellType is not a factor. Converting to factor with alphabetical levels.
The text was updated successfully, but these errors were encountered:
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Reprex:
If we check the
obj
structure, we will see that theIntegrateLayers
function didn't add the 'integrated' assay toobj
, which is already alarming:Instead, the SCT slot contains two SCTmodel(s), and I don't know how to join them, to be honest.
The problem arises when we want to generate Azimuth reference from this integrated object:
The text was updated successfully, but these errors were encountered: