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Published 20 hours ago • verified publisher icon dpeerlab

RuntimeWarning: divide by zero encountered in true_divide dists = dists ** 2/(scaling_factors.values[rows] ** 2)

Open fangfang0906 opened this issue 2 years ago • 1 comments

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?

fangfang0906 avatar Mar 08 '22 02:03 fangfang0906

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?

ManuSetty avatar Mar 08 '22 16:03 ManuSetty