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Batch effect issue for multiple 10X visium samples #54

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archanabhardwaj opened this issue Nov 9, 2022 · 1 comment

archanabhardwaj commented Nov 9, 2022

Hello

I am having batch effect issue for running multiple sample clustering in spaGCN as indicated in previous post #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

Author

archanabhardwaj commented Jan 16, 2023

For integrated samples , I used following steps :

QC Filteration
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 ?

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