DUBStepR doesnt work after Seurat Update!

[PaplomatasP]

Hello, Dear Maintainer ,

I used DUBStepR, but now I am encountering this error message: "Determining optimal feature set... Error in ScaleData(): No layer matching pattern 'data' found. Please run NormalizeData and retry. Run rlang::last_trace() to see where the error occurred." When I run rlang::last_trace(), I get the following error: "Error in ScaleData(): No layer matching pattern 'data' found. Please run NormalizeData and retry." The backtrace is as follows:

1
└─DUBStepR::DUBStepR(input.data = as.data.frame(NormalizeData(Input@assays$RNA$counts)))
3.   └─DUBStepR:::getOptimalFeatureSet(...)
4.     ├─base::suppressWarnings(...)
5.     │ └─base::withCallingHandlers(...)
6.     ├─Seurat::ScaleData(...)
7.     └─Seurat:::ScaleData.Seurat(...)
8.       ├─Seurat::ScaleData(...)
9.       └─Seurat:::ScaleData.StdAssay(...)
10.         └─rlang::abort(paste0("No layer matching pattern '", olayer, "' found. Please run NormalizeData and retry"))          

The problem is the same if you run the package example res <- DUBStepR(input.data = pbmc_norm_small_data). i think the problem is about the update of Seurat packages, and many thinks are changed. Do you think could you correct the problem ?

Thanks in Advance ,

Petros

[big-anime]

I have the same problem

[iaradsouza1]

I had to downgrade to seurat v4 and it worked. Apparently, this error is related to the Assays object from the SummarizedExperiment package.

One also needs to downgrade the SeuratObject package to the version 4.

Also, the corSparse function from the qlcMatrix version 0.9.7 is required to run the DUBStepR function. The qlcMatrix has been recently archived by CRAN, so it needs to be manually installed.