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dpeerlab / Harmony

Harmony framework for connecting scRNA-seq data from discrete time points
GNU General Public License v2.0
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RuntimeWarning: divide by zero encountered in true_divide dists = dists ** 2/(scaling_factors.values[rows] ** 2) #20

Open fangfang0906 opened 2 years ago

fangfang0906 commented 2 years ago

Dear authors,

Thanks for developing harmony! It's really cool! I got this warning "RuntimeWarning: divide by zero encountered in true_divide " when following standard pipeline and the embedding looks a little weird.

Screen Shot 2022-03-07 at 8 28 38 PM

Do you have any idea what's the possible reasons?

ManuSetty commented 2 years ago

Thank you for interest in Harmony. A could of questions:

  1. Do you encounter this issue with the example dataset too?
  2. Do you have any cells with 0 counts for all genes in our dataset?