Error when using the web app for PBMC annotation

[aaronejaime]

Hello everyone.

Im having some trouble loading data into the web app of Azimuth. Previously in RStudio Ive created a RDS file and then try to loading it into Azimuth but it throws the following error "No RNA assay provided".

When I look for the assays into my Seurat Object:

obj@assays

$RNA
Assay (v5) data with 17222 features for 7615 cells
Layers:
counts, data, scale.data

I am not sure how to fix this or if I don't even have to fix or specify something. Anybody can help?

[ryland-mortlock]

Getting the same error. My .rds file is a merged seurat object using seurat v5

[ryland-mortlock]

Seems like the web version still has the same issue. "No RNA assay provided." when using v5 seurat object

[jdime]

I'm getting the same issue using Seurat_5.0.1 to make the surat object.
Has anyone been able to fix/work around this?
Thanks.

[jdime]

In case anyone needs it. Here is a workaround. Instead of using a Seurat Object, I used a h5Seurat.
library(SeuratDisk)
so[["RNA"]] <- as(object = so[["RNA"]], Class = "Assay")
SaveH5Seurat(so, file ="~/path_to/file.h5seurat")

[aaronejaime]

In my case, when using an integrated object I firstly join the layers as Azimuth doesn't seem to accept multiple layers objects:
integrated.joined<-JoinLayers(integrated.object)

Following, extract assay matrix
integrated.matrix<-as.matrix(GetAssayData(integrated.joined, layer = 'counts')[, WhichCells(integrated.joined)])

And then put it in a RDS file:
saveRDS(integrated.matrix, file = "integrated-matrix.rds")