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I am preparing a rebuttal letter to reviewers and the editor about one of my manuscripts. The reviewers were concerned about the results and they suggest running the same models but using another way to calculate the response variable. I am totally fine to explore the data with other ways to make results more robust and reliable. However, the results from the methodology suggested by the reviewers are not the same as the other one. This makes me feel dubious about the conclusion drawn from my results.

Although in the first version of the manuscript I had a sharp conclusion based on the initial results, now I realized that I should tone down the message after exploring the data in different ways.

I was wondering if you had a similar experience like this and how did you manage to your rebuttal letter?

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    I think this needs a deeper look to analyze what you should take from this: what does it mean that the results are "not the same"? p<0.05 one way and p>0.05 another way? What happens to relevant confidence intervals: are they consistent? What is the interpretation of the differences in analysis approach? What are the implications for type I/II errors when using multiple statistical approaches?
    – Bryan Krause
    Sep 22 at 15:48

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It seems like a case in which the reviewers made good suggestions which made you go over your data and conclusions again, thereby improving your manuscript and saving you from making too bold claims. Therefore, the obvious approach is to thank the reviewers for their input and explain to the editor how your analysis and conclusions have changed/improved in the revised version of the manuscript by following the reviewers' advice. The way you explain it, your previous conclusions were not totally wrong. If so, you have no real reason to be overly worried just now. Focus on explaining your revisions to convince the editor that your manuscript is fit for publication.

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  • Thanks @Snijderfrey for the answer! Yep, I actually cannot hide from the suggestions of the reviewers since they are totally fair. It makes sense to not overstate my conclusions after re-analyzing my data. Thanks again!
    – Rinot
    Sep 22 at 12:26
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I think you are jumping the gun by thinking about the rebuttal letter. Your first priority here should be thinking about how these new results affect your paper and its conclusions. Rewrite your paper as needed, maybe even run further additional tests to confirm your new conclusions.

Now that you have written a better paper, writing a response to the reviewers (thinking about this as a "rebuttal" is already a wrong antagonistic mindset) is easy. Simply describe what you have done with the reviewers' suggestions and how this has improved your paper.

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  • Thanks @TimRias for the advice! Will take into account
    – Rinot
    Sep 23 at 12:26

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