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Downsampling is notorious for getting rid of hot pixels. Removing over half of the pixel count is bound to make things look better than they are at 36mp 100% crop. A D4 is only 16mp to start with, so thats by far the "truest" representation of ISO performance.
I ticked the option to down-sample all the files to 15mp raws. The purpose of this is to end up with raws that have the same output resolution as each other. This will give a more accurate representation of the noise, and better simulates what you would get in the real-world if you made 'X' size prints from each of the camera's.
Obviously, see the above quote.
This is why if your going to compare camera's noise performance, you first normalise the output size. Comparing pixel level noise of camera's with vastly different resolutions doesn't tell you anything about the quality of the final output (which is the important bit).
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