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I have two papers on the same data, but each gave me different results as I used different methods. I sent one of them to a journal and am waiting for the response which may take months.

The problem is that I need to publish the second one, which gave me a better result, at a conference. If it is accepted it will be published before the first one that I sent to the journal.

The question is: will the publication of the second one (at a conference) affect the journal's decision about the first one?

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    Better means nothing, if you do not clarify in which sense. Two methods to process the same dataset, it looks like they are independent papers. However, if the second paper method is really better, maybe you should stop the reviewing process of the first paper: it is a waste of time if you found a better method. On the other hand, if the first paper is presenting some theoretical study and the dataset is used only for validation of the theoretical study, it may be the case that it is worthwhile to publish it.
    – EarlGrey
    Aug 18, 2022 at 7:59

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Questions you need to ask yourself to answer 'yes':

Did you split one paper into two to get more papers? Do both papers heavily cite each other? Do the policies of the Journal or Conference explicitly forbid something like this?

Questions you need to ask yourself to answer 'no':

Are both papers completely independent of each other? Do they use the same data but make independent interpretations? Can a reader read any one before the other without having to ask for clarification?

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