Hello everyone
I'm currently dealing with spatial transcriptome data using the Xenium platform, where each slide contains several tissue sections.
1) Initially, I conducted separate analyses for each sample and identified numerous clusters of interest.
2) Now, I'm aiming to integrate these multiple samples, removing batch effects, and performing integrative cluster analysis. Should I adopt strategies similar to those used in single-cell analysis for multiple samples?
3) Regarding cluster annotation, some studies have utilized a marker-based approach. Would it be acceptable for Xenium if I utilize single-cell data for cell type annotation ?
I'm new to working with Xenium and want to ensure the approach I take for steps 2 and 3 is appropriate.
I would appreciate all the suggstions.
