Check for batch effect on data acquired with Rhapsody

[algebio]

Hello.

I have a dataset from a Rhapsody analyzer and I'm trying to check for batch effect on the control samples. The first problem I had was to adapt the files because they come in a different format, so I splitted the original file and I created a file with ADT data only and another with RNA only. Then I followed the tutorial for Seurat v4 "Using Seurat with multimodal data" to plot UMAPs.

My first question is: Is this the right way to use Rhapsody data in a Seurat pipeline?
My second question is: How can I colour the UMAP by batch?

Thank you for your help.

[timoast]

My first question is: Is this the right way to use Rhapsody data in a Seurat pipeline?

Seurat requires a matrix with features in the rows and cells in the columns to create an assay, if that's what you've generated than that's the correct data format.

My second question is: How can I colour the UMAP by batch?

Use the group.by argument in DimPlot(), and see the documentation for DimPlot() for more information