Question about <NA> labels from cell clustering via SC3

hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

http://bioconductor.org/packages/SC3

GNU General Public License v3.0

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Question about <NA> labels from cell clustering via SC3 #111

Closed yxy92 closed 6 months ago

yxy92 commented 6 months ago

Not sure if this is bug or more case-specific problem. I am using SC3 for cell clustering benchmark purpose, and when I tested it on a PBMC14K dataset with specified number of clusters k=7 from true labels. SC3 finishes clustering, with >50% of cells assigned with cluster label . There is no error message. How should I interpret this result or modify the argument running SC3. What causes from a consensus clustering?

mhemberg commented 6 months ago

Thanks for your request. Unfortunately, does not handle datasets with 14k cells very well, and as the software is no longer actively maintained, I do not think it is fair to include it in a benchmark. Instead, I advice that you use the new SC3s version which was developed to handle larger datasets.