Xenium spatial RNA-seq
Processing steps
Xenium features negative control probes and codewords that can be used to assess the quality of algorithms. It’s a good idea to check these periodically to see if they are driving anything such as clustering or differential expression.
Cell segmentation
Xenium’s default is often out-performed by 3rd party tools. FHIL prefers Proseg as it was developed by our collaborator.
Cell filtering
Clustering
Focusing on highly SVF may help clustering algorithms perform better. Review the selcetion of SVFs to minimize negative control probes.
Other processing steps
Log-transformation & normalization Use all PCs in graph formation