scRNA intergration

[rmauron]

Hi,
Could you please show me the shape the Seurat object should have for the point "8.1: Cross-platform linkage of scATAC-seq cells with scRNA-seq cells".
I tried to create a seurat object from my "filtered_feature_bc_matrix.h5" and take only the "Gene expression" to create my seurat object. But it doesn't work.
So if you could tell me how it should look I could maybe overcome this point.

Thanks in advance for your help!

[rcorces]

You can look at the code of addGeneIntegrationMatrix() and see what aspects of a Seurat object are used. I believe the primary requirements are:

1. Needs to have assay named "RNA" ("RNA" %in% names(seuratRNA@assays))
2. Needs to have a column in meta.data named for whatever you pass to the groupRNA param ([email protected][,groupRNA])

[rmauron]

Hi, thanks for the reply.
Now it seems to run but for some reasons it breaks saying "Error in sample.int(length(x), size, replace, prob) :
too few positive probabilities".

I attach my log file:
ArchR-addGeneIntegrationMatrix-ba2116114a737-Date-2023-02-22_Time-11-02-20.log

I don't understand what it stands for. My Seurat object seRNA has meta.data and I gave the "groupRNA" different columns from it and I always get the same output.

I hope my issue is clear

[rcorces]

I'm afraid I dont have enough information to help you