Error with DefaultAssay in R when Integrating Data Using scvi-tools

Help scvi-tools
,
1

Hello,

I am encountering an issue while trying to integrate data using scvi-tools in R. Here is the code I am using:

R

latent <- as.matrix(latent)
rownames(latent) = colnames(adata)
adata[["scvi"]] <- CreateDimReducObject(embeddings = latent, key = "scvi_", assay = DefaultAssay(adata))

However, this results in the following error:
Error in UseMethod(generic = “DefaultAssay”, object = object): no applicable method for ‘DefaultAssay’ applied to an object of class “c(‘anndata._core.anndata.AnnData’, ‘python.builtin.object’)”
Traceback:

  1. CreateDimReducObject(embeddings = latent, key = “scvi_”, assay = DefaultAssay(adata))
  2. DefaultAssay(adata)

t seems that the DefaultAssay function is not recognizing the adata object as expected. I have confirmed that adata is an AnnData object.

version：
r-seurat 4.4.0
scvi-tools 1.1.2

Could you please help me understand what might be causing this error and how to resolve it?

Thank you!

2

I’m not really an expert for Seurat. However, from the error latent contains an AnnData object and not a matrix. Can you provide the data type of latent?

3

Thank you very much for your reply, and I apologize for the delay in getting back to you. You were correct, I checked the format of latent and adata, and the issue was indeed there. The error has been resolved, thank you so much.

However, I have encountered a new problem. When running

ifnb <- RunUMAP(ifnb, dims = 1:10, reduction = "scvi", n.components = 2),

I get the error Error in irlba::irlba(L, nv = n, nu = 0, maxit = iters): function 'sexp_as_cholmod_sparse' not provided by package 'Matrix'.
My Matrix version is [1] ‘1.6.1.1’. Do you know which version of Matrix provides sexp_as_cholmod_sparse?
Thank you again for your reply!

4

This is more a question to the Seurat (or matrix) developers and I wouldn’t expect a response her, unfortunately.

5

ok, I’ll try to solve it focusing on Seurat and Matrix, thanks a lot!