Open chungsai opened 7 months ago
Using the exact code from the module https://satijalab.org/seurat/articles/seurat5_integration,
Using the exact libraries, but replaced the first steps with the code in the bottom for SCTransform
obj <- SCTransform(obj) obj <- RunPCA(obj, npcs= 30, verbose = FALSE) obj <- RunUMAP(obj, dims = 1:30, verbose = FALSE, reduction.name = "umap.unintegrated") obj <- FindNeighbors(obj, dims = 1:30, verbose = FALSE, reduction = "pca") obj <- FindClusters(obj, resolution =2, verbose = FALSE, cluster.name = "unintegrated_clusters")
Then.
obj <- IntegrateLayers( object = obj, method = CCAIntegration, normalization.method = "SCT", new.reduction = "integrated.cca", verbose = F )
obj <- IntegrateLayers( object = obj, method = RPCAIntegration, normalization.method = "SCT", new.reduction = "integrated.rpca", verbose = F )
obj <- IntegrateLayers( object = obj, method = HarmonyIntegration, normalization.method = "SCT", new.reduction = "Harmony", verbose = F )
obj <- IntegrateLayers( object = obj, method = FastMNNIntegration, normalization.method = "SCT", new.reduction = "integrated.mnn", verbose = F )
Integration works well until FastMNN. It gives me the error
It seems like a bug similar to this was known before?
https://github.com/satijalab/seurat/issues/5329
I tried the FastMNN code edit by user yuanlizhanshi before. However, it made no difference.
I am wondering if anyone has resolved this issue.
Thanks,
Hi @chungsai,
I'm having the same issue but with my own data. Did you ever find a fix for it?
KR
Using the exact code from the module https://satijalab.org/seurat/articles/seurat5_integration,
Using the exact libraries, but replaced the first steps with the code in the bottom for SCTransform
obj <- SCTransform(obj) obj <- RunPCA(obj, npcs= 30, verbose = FALSE) obj <- RunUMAP(obj, dims = 1:30, verbose = FALSE, reduction.name = "umap.unintegrated") obj <- FindNeighbors(obj, dims = 1:30, verbose = FALSE, reduction = "pca") obj <- FindClusters(obj, resolution =2, verbose = FALSE, cluster.name = "unintegrated_clusters")
Then.
obj <- IntegrateLayers( object = obj, method = CCAIntegration, normalization.method = "SCT", new.reduction = "integrated.cca", verbose = F )
obj <- IntegrateLayers( object = obj, method = RPCAIntegration, normalization.method = "SCT", new.reduction = "integrated.rpca", verbose = F )
obj <- IntegrateLayers( object = obj, method = HarmonyIntegration, normalization.method = "SCT", new.reduction = "Harmony", verbose = F )
obj <- IntegrateLayers( object = obj, method = FastMNNIntegration, normalization.method = "SCT", new.reduction = "integrated.mnn", verbose = F )
Integration works well until FastMNN. It gives me the error
It seems like a bug similar to this was known before?
https://github.com/satijalab/seurat/issues/5329
I tried the FastMNN code edit by user yuanlizhanshi before. However, it made no difference.
I am wondering if anyone has resolved this issue.
Thanks,