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error in scVIIntegration when using SCTransform #209

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wanghf810501 opened this issue Dec 28, 2024 · 0 comments
Open

error in scVIIntegration when using SCTransform #209

wanghf810501 opened this issue Dec 28, 2024 · 0 comments

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@wanghf810501
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I encounter the following error messages
"Error in UseMethod(generic = "JoinLayers", object = object): no applicable method for 'JoinLayers' applied to an object of class "c('SCTAssay', 'Assay', 'KeyMixin')""
When I try to run the example code for scVIIntegration, the code is as following:
obj <- SeuratData::LoadData("pbmcsca")
obj[["RNA"]] <- split(obj[["RNA"]], f = obj$Method)
obj <- SCTransform(object = obj)
obj <- RunPCA(obj)
obj <- IntegrateLayers(
object = obj, method = scVIIntegration,
orig.reduction = "pca", new.reduction = "integrated.scvi",
assay = "SCT", conda_env = "/home/wanghf/anaconda3/envs/scvi-env", verbose = FALSE
)

I am using seurat 5.1.0, so could you please help me to solve the problem?

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