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TomKellyGenetics / DoubletDetection

Doublet detection in single-cell RNA-seq data (R package).
MIT License
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No doublets identified with default thresholds #2

Open TomKellyGenetics opened 6 years ago

TomKellyGenetics commented 6 years ago

Doublets are only identified with relaxed p-value thresholds (not the default of p <=0.01). While these are significantly enriched for doublets identified by the Python implementation (by Fisher's Exact Test), many different cells are identified in the same datasets.

adamgayoso commented 6 years ago

You should try not scaling the data when calling PCA. sklearn implementation only centers the data.

TomKellyGenetics commented 6 years ago

I've updated this to be consistent with the Python version. Unfortunately, the issue persists and the results are still considerably different.