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Bias/dark calibration doesn't remove shot noise. It removes unwanted signal, i.e. bias pedestal and thermal noise. In fact, it adds a little shot noise that remains in the master calibration files.
The superbias process takes a poor quality master bias and "improves" it by doing multiscale noise reduction. The superbias will add less shot noise during calibration than the poor master bias, but it won't be quite as effective at removing unwanted signal. I think this remaining unwanted signal is probably what you're measuring.
I'm not a big fan of superbias. I'd much rather build a good quality master bias based on a large number of bias frames.
Cheers,
Rick.
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