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I am middle author of a manuscript that has been submitted and received reviews asking for some additional analyses. Two of the authors (including the PI) prepared the revision, sent it to the other authors (5-7 in total), asking for comments and suggestions.

I had a very different interpretation of the results of the additional analysis, and in my opinion, the conclusion in the revised manuscript is wrong, due to the authors (i.e. those that prepared the revision) ignored the results of the additional analysis. I pointed this out in an email to the other authors, and gave my interpretation of the results. There was no direct reply to my email, however one week later the "updated" manuscript was sent to me, and submitted to the journal the same day. There was no proper chance to react to this "updated" version, and obviously, the submitted revision was not approved by me. More importantly, the "updated" version contained the same mistakes, ignoring the results of the additional analysis, and thus, ignoring my comments.

Any suggestions how I should deal with this? It feels like contacting the PI/corresponding author won't lead anywhere. Should I contact the editor directly?

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    They may not have read your email. You should talk to the PI. – Anonymous Physicist Jun 26 '17 at 1:35
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    If you want to keep a good working relation with the PI, don't contact the editor directly! Your issue has to be dealt within your project/publication team, so yes, contact the PI and ask for a face2face talk on the paper (not another email conversation) and your concerns. – Stefan_W Jun 26 '17 at 11:37
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    If you do contact the editor, he'll ask you what the PI told you. And then, what will you tell the editor? "I don't know. He never replied to my email." Is that really your plan of action? You need to talk to the PI first. Call him, sms, email, have a friend drop by his office, and/or send him a FedEx letter with signature required. You need to try everything you can to talk to him. The PI may try to avoid your calls, lie to you, tell you that he doesn't agree with you, or concede that you were right -- but that he didn't have the time. Whatever is his excuse, you need to know what it is. – Stephan Branczyk Jun 26 '17 at 12:04
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    @StephanBranczyk In the end, the PI replied to me, saying that he doesn't agree with my points, and thus decided to submit the manuscript. The reaction to my concerns are to some extend similar to his reactions to the reviewers' concerns, possibly because all alternative interpretations (e.g. the one I offer) go against his hypothesis. Therefore, I would not be surprised if the manuscript will be rejected or send back for another round of revision. – Mark Jun 26 '17 at 23:48
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    @Mark Personally, I'd be less concerned about the manuscript being rejected, and more concerned about it being accepted with what you think are inaccurate conclusions. Would that be something you're personally okay with, given the particular scope and extent of the mis-analysis? If not, you really need to sit down with the corresponding author (I mean that literally) and hash it out. They may disagree with your viewpoint, but you need to get to the point where you both agree to disagree. – R.M. Jun 28 '17 at 14:39
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I have had this kind of conflict before, and I believe the issue is much more common than reported. I believe most colleagues in your position would (i) not have offered a different interpretation from that of the PI; (ii) not protest in case others ignored their suggestions. This is generally what was suggested in this thread by "move on".

I however do not agree with this passive approach if you are truly an author involved in the manuscript. I think all co-authors should reach a logical agreement over the results. My suggestions in this case are based on a personal choice based on details I cannot evaluate:

(A) If you believe their interpretation might be right even though you (and reviewers) see facts in a different way, just let them have it their way. "Move on". You can make your different views public later on in a subsequent publication or even post-publication peer review discussion forum. Your career is longer than this study.

(B) If you believe there is an obvious flaw in the PI's thinking that will be ridiculed by your peers after publication, ask to be removed from the authors list of this manuscript. I believe once you make this decision known to the PI there will be a moment of crisis, especially since this person submitted a revised version without your consent. However it will be a lesson for everyone, you will be not doing anything harmful to anyone (your name can be moved to the acks section without major issues prior to final publication), and everyone's career is longer than this discussion.

By now you have probably made your decision, but I hope this answer helps others decide.

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I feel it is too lithle too late. Let the first author learn from the rejection instead. Or, you will have another round of revision and have a chance to revise the analysis. Otherwise, move on!

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