It is recommended to use RPCA reduction when running FindIntegrationAnchors on large dataset by Seurat authors. However when I do this, I get error Error: Cannot find 'pca' in this Seurat What should I do to get rid of this error? should...
Error: Cannot find 'umap' in this Seurat object I haven't made any changes to the code or the data since a month ago. I also re-downloaded the data, Seurat today in order to make sure everything was up to date (just FYI, I tried the newest Seurat v4.0 as well as v3.2.2), b...
Recently, 'Matrix' package seem to be hugely changed, > KTM_seu_sub <- FindNeighbors(KTM_seu_sub, reduction = "pca", dims = 1:40) Computing nearest neighbor graph Computing SNN Error in validityMethod(as(object, superClass)) : object 'Cs...
reference object is a SCT normalized data in seurat version 3.2.0 When I use FindTransferAnchors function in seurat version 3.9.9, it report error: Error in as.data.frame.default(x) : cannot coerce class ‘structure("SCTModel", package = "Seurat")’ to a data.frame Due to different ve...
(Error: Cannot add different number of cells than already present ) on the normalization step. I've read multiple issue pulls and etc and still have no idea why it's occurring. I've checked the seurat object itself and see that the original number of cells 59824 matches with the object[...
Hi, Thanks for developing this great tool. I'm running into an error in LoadH5Seurat() step, stated that: Error: Missing required datasets 'levels' and 'values'. My data was downloaded from here: https://drive.google.com/file/d/1IwWcn4W-...
Error in as.data.frame.default(x) : cannot coerce class ‘structure("SCTModel", package = "Seurat")’ to a data.frame Thanks for sending this object. There is a bug inUpdateSCTAssays. Currently, you can useasto convert integrated assay fromAssaytoSCTAssay. Because it was integrated in ...
I have updated this in the attached file. The number of dubious cells still does not match the tutorial exactly; it turns out that using the default Seurat RunPCA(object, npcs = 50) and then subsetting to K dimensions is not the same as RunPCA(object, npcs = K). This seems to be...
Hello! I am wanting to run AddModuleScore() to an integrated dataset (I used the non-SCTransform pipeline), but it returns the following error: Error in sample.int(length(x), size, replace, prob) : cannot take a sample larger than the po...
Description: I encountered an error while using the selection.method = "moransi" option in the SpatiallyVariableFeatures() function. The error message states: "Error in xtfrm.data.frame(x) : cannot xtfrm data frames." This issue arises w...