Selection of integration variable in spatial transcriptomics: slide vs. donor #8485
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sallyseullee-0821
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Hi, I hope everyone reading this is having a great day.
I am working with spatial transcriptomics data from four slides, each containing tissues from two different donors (totaling 8 donors). After normalizing the data for each slide, I combined all slides into a single Seurat object.
My challenge now lies in deciding the best integration strategy: should I integrate across the eight donors or treat each four slides as separate batches to account for potential non-biological batch effects?
What are the recommended practices for integration in such scenarios?
Thank you in advance for your insights!
Sally
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