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I published a peer-reviewed article several years ago. Recently when I look back on my paper, I suddenly realized there had a figure duplication problem in one of the main figures (That main figure has more than 20 sub-figures, I only have a duplication problem in two cases). What is worse, the original data is lost due to the broken laptop (This is a great lesson I have learned) so the original data is not available anymore.

However, (1) I can run an experiment again to show the same outcome; (2) this mistake does not hurt the main conclusion; (3) and the result has been validated by other groups. I am wondering in such a situation, should I talk with my mentor, rerun the experiment, update the figure, and ask for a correction for this paper. Or I should ask for a withdrawal since I can not provide the raw data anymore (I have seen the author retract their papers because of unavailable raw data e.g., https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2045615/).

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You should definitively discuss this with your mentor, who presumably knows the conventions of your field. If conventions or journal policy are still unclear at that point you can always check with an editor of the journal what course of action they do prefer.

Take the following with a dose of salt, because my physics perspective probably isn't to be trusted in your case given that you linked to a medical journal. However, I'd think that if you can repeat the experiment (with proper approvals in place) to fix the mistake, and the mistake doesn't invalidate the main conclusion, then an erratum/corrigendum is probably the better outcome for all parties. The International Committee of Medical Journal Editors has some guidelines on how journals should handle corrections and retractions, which seems to agree with my position:

Pervasive errors can result from a coding problem or a miscalculation and may result in extensive inaccuracies throughout an article. If such errors do not change the direction or significance of the results, interpretations, and conclusions of the article, a correction should be published that follows the minimum standards noted above.

Errors serious enough to invalidate a paper's results and conclusions may require retraction. However, retraction with republication (also referred to as “replacement”) can be considered in cases where honest error (e.g., a misclassification or miscalculation) leads to a major change in the direction or significance of the results, interpretations, and conclusions.

If even pervasive errors can be handled as an erratum, probably your case can too. Finally, here's an example of an erratum fixing a rather large image duplication problem by repeating the experiments. Also see this Retraction Watch post.

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  • thanks a lot for your notes. I published a journal belongs to nature groups. I have checked their policy but do not found a clear clue how to deal with such a situation. nature.com/nature-research/editorial-policies/…. It seems like there has an enormous gray area between retraction and correction. Also, I have tried to contact my supervisor weeks ago but he kept quiet yet. Not sure should I just hide the mistake and move on or I should try my best to make it face to the public. I sweat in these days because of this issue.
    – whatshouldIdo
    May 26, 2020 at 18:05
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    @whatshouldIdo Yes, there's a grey area, largely because every case is slightly different. However, don't try to hide the mistake. That's never the right or honest approach, and you might end up featured in some less flattering online discussions, like in the Retraction Watch post I linked. It always looks better if you address your mistakes before someone else points them out.
    – Anyon
    May 26, 2020 at 18:35
  • Thanks, Anyon. If I would like to do the correction, should I re-do the experiment firstly and ask for the correction. Or I should ask for correction firstly and with their permission I can re-run the experiment. I do not mind running the same experiment multiple times to increase the chance to get a higher chance for correction. Also, my supervisor stays really cold with me and I have a hard time communicating with him (I am not sure if he will retract the paper to protect his scientific integrity). If you were me, would you still suggest facing this problem as we planed?
    – whatshouldIdo
    May 26, 2020 at 19:40

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