search

SingleR-inc / SingleR

Clone of the Bioconductor repository for the SingleR package.
https://bioconductor.org/packages/devel/bioc/html/SingleR.html
GNU General Public License v3.0
177 stars 19 forks source link

How to use SingleR for integration analysis in Seurat? #185

Closed lkqnaruto closed 3 years ago

lkqnaruto commented 3 years ago

Hi

I'm currently working on the cell type annotation task using Seurat, where I have 3 samples for control group, 8 samples for treatment group, and I would like to know the cell type for each group. Then I integrated the samples within each group.

I have a question regarding to SingleR: After I got integrated data, should I pass the integrated assay data to SingleR? or the RNA assay data to SingleR?

During the diagnostic step, would it be always better to use prune label column? rather than label column.

Thanks

LTLA commented 3 years ago

Pass the raw counts, see the discussion in #98.

The prune.label column is just a more conservative version of label. It assumes that, for the set of cells assigned to a given label, the majority of them are correctly assigned, and it will trim away the calls with relatively poor scores. It won't provide much protection against major errors, e.g., when the true cell type is not in the reference so SingleR assigns it to the closest matching type.

lkqnaruto commented 3 years ago

Thank you for the response. The discussion in #98 is great to learn.

Just want to double check, the raw counts is located at the integrated Seurat object, RNA assay, slot counts, right? I'm using the latest version of Seurat, btw.

j-andrews7 commented 3 years ago

Yes, that's correct as far as I remember.

lkqnaruto commented 3 years ago

@j-andrews7 Thank you for the reply