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

**URL:** <https://discourse.scverse.org/t/error-with-defaultassay-in-r-when-integrating-data-using-scvi-tools/2333>\
**Category:** scvi-tools\
**Tags:** integration, scvi\
**Created:** [June 14, 2024, 7:27am UTC](https://discourse.scverse.org/t/error-with-defaultassay-in-r-when-integrating-data-using-scvi-tools/2333 "2024-06-14T07:27:57Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![xiaoshanji](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/xiaoshanji/32/1077_2.png) [@xiaoshanji](https://discourse.scverse.org/u/xiaoshanji)\
**Post date:** [June 14, 2024, 7:27am UTC](https://discourse.scverse.org/t/error-with-defaultassay-in-r-when-integrating-data-using-scvi-tools/2333/1 "2024-06-14T07:27:57Z")

</div>

Hello,

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

R

```auto
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!

---

<div class="post-metadata">

**Author:** ![cane11](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/cane11/32/241_2.png) [@cane11](https://discourse.scverse.org/u/cane11)\
**Post date:** [June 19, 2024, 3:31am UTC](https://discourse.scverse.org/t/error-with-defaultassay-in-r-when-integrating-data-using-scvi-tools/2333/2 "2024-06-19T03:31:42Z")

</div>

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?

---

<div class="post-metadata">

**Author:** ![xiaoshanji](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/xiaoshanji/32/1077_2.png) [@xiaoshanji](https://discourse.scverse.org/u/xiaoshanji)\
**Post date:** [July 15, 2024, 4:51am UTC](https://discourse.scverse.org/t/error-with-defaultassay-in-r-when-integrating-data-using-scvi-tools/2333/3 "2024-07-15T04:51:54Z")

</div>

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!

---

<div class="post-metadata">

**Author:** ![cane11](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/cane11/32/241_2.png) [@cane11](https://discourse.scverse.org/u/cane11)\
**Post date:** [July 15, 2024, 6:46am UTC](https://discourse.scverse.org/t/error-with-defaultassay-in-r-when-integrating-data-using-scvi-tools/2333/4 "2024-07-15T06:46:44Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![xiaoshanji](https://yyz1.discourse-cdn.com/flex035/user_avatar/discourse.scverse.org/xiaoshanji/32/1077_2.png) [@xiaoshanji](https://discourse.scverse.org/u/xiaoshanji)\
**Post date:** [July 16, 2024, 5:54am UTC](https://discourse.scverse.org/t/error-with-defaultassay-in-r-when-integrating-data-using-scvi-tools/2333/5 "2024-07-16T05:54:45Z")

</div>

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