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Thanks a lot
I am leating seurat v5.
In https://satijalab.org/seurat/articles/integration_introduction,
joinlayers used after immediately after
ifnb <- IntegrateLayers(object = ifnb, method = CCAIntegration, orig.reduction = "pca", new.reduction = "integrated.cca",
verbose = FALSE)
re-join layers after integration
ifnb[["RNA"]] <- JoinLayers(ifnb[["RNA"]])
would this order matters the final result ot other following analysis?
I know there is one sentense
"Once integrative analysis is complete, you can rejoin the layers - which collapses the individual datasets together and recreates the original counts and data layers. You will need to do this before performing any differential expression analysis. However, you can always resplit the layers in case you would like to reperform integrative analysis"
what I am exampling here all are after IntegrateLayers, what I am puzlling about is immediately after IntegrateLayers or not
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Thanks a lot
I am leating seurat v5.
In https://satijalab.org/seurat/articles/integration_introduction,
joinlayers used after immediately after
ifnb <- IntegrateLayers(object = ifnb, method = CCAIntegration, orig.reduction = "pca", new.reduction = "integrated.cca",
verbose = FALSE)
re-join layers after integration
ifnb[["RNA"]] <- JoinLayers(ifnb[["RNA"]])
but in https://satijalab.org/seurat/articles/seurat5_integration,
joinlayers used after
obj <- IntegrateLayers(
object = obj, method = CCAIntegration,
orig.reduction = "pca", new.reduction = "integrated.cca",
verbose = FALSE
)
obj <- FindNeighbors(obj, reduction = "integrated.cca", dims = 1:30)
obj <- FindClusters(obj, resolution = 2, cluster.name = "cca_clusters")
obj <- RunUMAP(obj, reduction = "integrated.cca", dims = 1:30, reduction.name = "umap.cca")
p1 <- DimPlot(
obj,
reduction = "umap.cca",
group.by = c("Method", "predicted.celltype.l2", "cca_clusters"),
combine = FALSE, label.size = 2
)
obj <- JoinLayers(obj)
obj
would this order matters the final result ot other following analysis?
I know there is one sentense
"Once integrative analysis is complete, you can rejoin the layers - which collapses the individual datasets together and recreates the original counts and data layers. You will need to do this before performing any differential expression analysis. However, you can always resplit the layers in case you would like to reperform integrative analysis"
what I am exampling here all are after IntegrateLayers, what I am puzlling about is immediately after IntegrateLayers or not
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