I ran an analysis three different ways and two methods support the hypothesis, but the third one weakens the result enough that the story becomes less clear. My supervisor immediately focused on the stronger outputs and barely wanted to discuss the weaker one. How do you handle it when you know the full picture is messier than what people want to present?

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That’s pretty normal for some fields
If there is a defensible reason to not use the weaker method (as in its weakness is from artifacts etc.) then it’s fine to ignore

Otherwise just be ready for someone to bring it up because they be probably will

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