Error: Cannot find 'pca' in this Seurat What should I do to get rid of this error? should I run RunPCA beforeFindIntegrationAnchorsandScaleData? In this case when should I useDefaultAssay Would it not change any outcome? Thank you Please run RunPCA() before you do RPCA based integration...
针对您提出的“error: cannot find 'umap' in this seurat object”问题,这里有几个可能的解决方案和检查步骤,帮助您解决这个问题: 确认'umap'是否已正确安装在环境中: 虽然UMAP通常作为Seurat包的一部分自动安装,但确保您的R环境中已安装并加载了Seurat包。您可以通过以下代码来安装和加载Seurat包: R if (!requi...
Error: Cannot find 'pca' in this Seurat object So I am stuck. Can you please look into what's causing this issue and recommend a fix? Many thanks.liu-xingliang commented Dec 16, 2021 I think what RunPCA is complaining is about the rank of the input matrix is not positive, which i...
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...
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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...
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-...
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...
(seurat_obj.ref, verbose = FALSE) seurat_obj.ref <- RunPCA(seurat_obj.ref, npcs = 30, verbose = FALSE) # must run PCA before FindTransferAnchors() anchors_obj <- FindTransferAnchors(reference = seurat_obj.ref, query = seurat_obj.query, dims = 1:30, reference.reduction = "pca") ...