Performing integration analysis of two datasets of different sizes in Seurat
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3.3 years ago
aa123 • 0

I am following the Satija Lab's ctrl vs stim Seurat tutorial (https://satijalab.org/seurat/v3.1/immune_alignment.html) to integrate two datasets. My stim dataset contains 1500 more cells than my ctrl dataset. Does this bias my analysis (finding anchors, clustering, visualization by UMAP, DE)? Is there a way that I can account for this in the downstream analysis?

Thank you

scrnaseq seurat • 918 views
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