Raw counts for scRNA-seq

[jnmark]

Are raw counts available for the scRNA-seq data? From the commands history in the Seurat object, seems like the data in the "RNA" slot under assays is normalized.

[massonix]

Hi @jnmark, you can access the counts as follows:

cd4  <- HCATonsilData(cellType = "CD4-T")
counts(cd4)

In the Seurat objects available in Zenodo, the counts are under seurat[["RNA"]]@counts.

Hope that helps!

[jnmark]

Thanks for the response! I have been using the combined Seurat object and trying to access the counts in the same way, but it seems like they are normalized and not raw, but I am looking for the raw counts.

On Thu, Sep 8, 2022, 3:18 AM Ramon Massoni-Badosa @.***> wrote:

Hi @jnmark https://github.com/jnmark, you can access the counts as follows:

cd4 <- HCATonsilData(cellType = "CD4-T") counts(cd4)

In the Seurat objects available in Zenodo https://zenodo.org/record/6340174#.YxmXE-xBz0o, the counts are under @.*** https://github.com/CountS.

Hope that helps!

— Reply to this email directly, view it on GitHub https://github.com/massonix/HCATonsilData/issues/7#issuecomment-1240324384, or unsubscribe https://github.com/notifications/unsubscribe-auth/ARKDXMYPEALBUFQUJ3DQDQDV5GHODANCNFSM6AAAAAAQHBS6KU . You are receiving this because you were mentioned.Message ID: @.***>

[jnmark]

Hello, I checked the individual cell Seurat objects as well, but they seem to be normalized too. Is there any way to get access to the raw counts? I am trying to use the scRNA-seq data for cell type deconvolution, and it would require me to have access to the raw counts.