Closed rojinsafavi closed 3 years ago
I am following your pbmc multiomic example (the same dataset as you provided in the toturial) And after running this block
# transfer cell type labels from reference to query transfer_anchors <- FindTransferAnchors( reference = reference, query = pbmc, normalization.method = "SCT", reference.reduction = "spca", dims = 1:50 )
I get this error:
Error in FindTransferAnchors(reference = reference, query = pbmc, normalization.method = "SCT", : unused argument (reference.reduction = "pca") Traceback:
Then I removed the reference.reduction , and re-ran:
# transfer cell type labels from reference to query transfer_anchors <- FindTransferAnchors( reference = reference, query = pbmc, normalization.method = "SCT", dims = 1:50 )
Error in vst.set[[x]]: subscript out of bounds Traceback: 1. FindTransferAnchors(reference = reference, query = pbmc, normalization.method = "SCT", . dims = 1:50) 2. GetResidual(object = reference, features = features, verbose = FALSE) 3. sapply(1:length(vst.set), function(x) rownames(vst.set[[x]]$model_pars_fit)) 4. lapply(X = X, FUN = FUN, ...) 5. FUN(X[[i]], ...) 6. rownames(vst.set[[x]]$model_pars_fit)
The Seurat v4 beta release is required: remotes::install_github("satijalab/seurat", ref = "release/4.0.0")
remotes::install_github("satijalab/seurat", ref = "release/4.0.0")
I am following your pbmc multiomic example (the same dataset as you provided in the toturial) And after running this block
I get this error:
Then I removed the reference.reduction , and re-ran:
I get this error: