Replies: 2 comments 3 replies
-
If you have tried this with Seurat4, can you ensure I cannot reproduce this at my end. Can you try: mouse <- LoadH5Seurat("Mouse_PR_clean.h5seurat", meta.data = FALSE, misc = FALSE, array = "RNA")
mouse <- UpdateSeuratObject(mouse)
mouse <- NormalizeData(mouse)
mouse <- FindVariableFeatures(mouse, nfeatures = 2000) and see if that fixes it? Also can you please report output of |
Beta Was this translation helpful? Give feedback.
-
I saw similar problem yesterday. The same coding worked 3 days ago (Seurat 5.0.0), but after updating to Seurat 5.0.1, it stopped working. Then I downgrade to Seurat 4.4.0, SeuratObject 4.1.14, another problem comes - "Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters) : function 'as_cholmod_sparse' not provided by package 'Matrix', which disallows the function of RunUmap. I am using a M1 chip. Can anyone help? |
Beta Was this translation helpful? Give feedback.
-
Hello,
Recently I have been getting an error, despite the code working in the past. The input data was not changed in any way and I noticed this error was occurring only after updating to Seurat 5.0.1. In addition, when running on a computer with Seurat 4.3.0 and Seurat Object 4.1.3, the code runs just fine. Below is the error:
#Converting from h5ad to h5seurat
Convert("Mouse_PR_clean.h5ad", dest = "h5seurat", overwrite = TRUE)
#Loading the h5seurat dataset
mouse <- LoadH5Seurat("Mouse_PR_clean.h5seurat", meta.data = FALSE, misc = FALSE, array = "RNA")
#Standard Pre-processing of Mouse Dataset
mouse <- NormalizeData(mouse)
mouse <- FindVariableFeatures(mouse, nfeatures = 2000)
Error in order(hvf.info$vst.variance.standardized, decreasing = TRUE) :
argument 1 is not a vector
To fix this error, I have been trying to degrade the Seurat version following the instructions on the seurat website, and although I converted Seurat and Seurat Object to the required lower versions, the error still persists, which may be because the CRAN dependency packages are still a higher version. Is this a correct interpretation of the error and how is it recommended to fix it? Thanks in advance!
Beta Was this translation helpful? Give feedback.
All reactions