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Doubets do not occupy distinct states

Open AAA-3 opened this issue 1 year ago • 0 comments

Code:

scrub = scr.Scrublet(counts_matrix, expected_doublet_rate=0.05) #range is 0.05-0.1.
doublet_scores, predicted_doublets = scrub.scrub_doublets(min_counts=2, 
                                                          min_cells=3, 
                                                          min_gene_variability_pctl=85, 
                                                          n_prin_comps=100, #set high since this is what I plan to use in Seurat
                                                         log_transform='TRUE') 
scrub.set_embedding('UMAP', scr.get_umap(scrub.manifold_obs_, 10, min_dist=0.3))
scrub.plot_embedding('UMAP', order_points=True);

287784_prob_density 287784_scrub_umap

My histograms seem normal, but the umap indicates that I have A LOT of doublets in my sample - would this be expected?

AAA-3 avatar Jan 23 '24 18:01 AAA-3