Batch effect issue for multiple 10X visium samples

[archanabhardwaj]

Hello

I am having batch effect issue for running multiple sample clustering in spaGCN as indicated in previous post https://github.com/jianhuupenn/SpaGCN/issues/37

Would you please help me if you can explain steps to perform z-score normalization for integrated dataset.

I would appreciate all the suggestion.

Thanks in advance

[archanabhardwaj]

For integrated samples , I used following steps :

1. QC Filteration
2. Integrated four samples with scanpy as suggested in https://nbisweden.github.io/workshop-scRNAseq/labs/compiled/scanpy/scanpy_07_spatial.html using scanorama method.

Is it ok if I run clf=spg.multiSpaGCN on the integrated adata object ?