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Vivianstats / scImpute

Accurate and robust imputation of scRNA-seq data
https://www.nature.com/articles/s41467-018-03405-7
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Part of the data not imputed #22

Open xianingz opened 5 years ago

xianingz commented 5 years ago

I randomly subsampled my counts data for imputing. The labels are known and there are four classes. When I tried 1000 or 1500 cells, it worked well. But when I tried 2000, there are two clusters of cells that are not imputed and it's three when I tried 3000. Is there anything wrong with my parameter setting? scimpute(counts.dat, infile = "txt", outfile = "txt", out_dir = outdir, labeled = TRUE, labels = labels, drop_thre = 0.5, ncores = 2)

zhengtaoxiao commented 5 years ago

Hi, the same problem happened to me. I think only the new version(0.09) have this problem. I tried the old one (v0.07), it worked well.

Vivianstats commented 5 years ago

Thank both for the reports. I am looking into this issue and will update you when it's fixed.

Vivianstats commented 5 years ago

The problem is now fixed in v0.09. Thank you very much for your comments!