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RuntimeWarning: divide by zero encountered in true_divide dists = dists ** 2/(scaling_factors.values[rows] ** 2) #20

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fangfang0906 opened this issue Mar 8, 2022 · 1 comment
Open

RuntimeWarning: divide by zero encountered in true_divide dists = dists ** 2/(scaling_factors.values[rows] ** 2) #20

fangfang0906 opened this issue Mar 8, 2022 · 1 comment

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@fangfang0906
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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
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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?

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@ManuSetty @fangfang0906