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carpenter-singh-lab / 2023_Cimini_NatureProtocols

Optimizing the Cell Painting assay for image-based profiling
BSD 3-Clause "New" or "Revised" License
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utils.percent_score: below_threshold not multiplied with 100 #17

Closed danr closed 1 year ago

danr commented 1 year ago

Hi!

I noticed that below_threshold is not multiplied with 100 in percent_score here: https://github.com/carpenter-singh-lab/2022_Cimini_NatureProtocols/blob/6b52a2775634dd2b496b137be21bf171c92672fb/notebooks/utils.py#L65

I believe this is correct the fix:

- return 100 * np.mean(above_threshold.astype(float)) + np.mean(below_threshold.astype(float)), perc_95, perc_5 
+ return 100 * np.mean(above_threshold.astype(float)) + 100 * np.mean(below_threshold.astype(float)), perc_95, perc_5

Perhaps this will impact the plots in the paper.

bethac07 commented 1 year ago

Oh my, yes, it sure looks like there was supposed to be parentheses there that certainly were not there!

I am going through and rerunning the affected notebooks now. My sincerest gratitude!