Integrated Seurat datasets

[AltayYuzeir]

Hello. I have a question regarding using LIANA with multiple integrated scRNA datasets, based on this tutorial: https://satijalab.org/seurat/articles/integration_introduction.html. Does the methods implemented in LIANA account for the differences such as sequencing technology or sequencing depth between the different datasets? Upon following the tutorial you get an "integrated" assay, but you need to run LIANA with the default "RNA" assay, as the "integrated" assay contains negative values.

[dbdimitrov]

Hi @AltayYuzeir, the integrated assay from Seurat is not typically intended to be used /w LIANA.

Instead, you should use the integrated assay to solely identify common cell clusters across your samples, and then use the log-normalized or SCT-normalized counts. As you will notice also from the tutorial, they switch back to the RNA assay right after integration.

[AltayYuzeir]

I see, thank you.