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Also, did you collect data with the same equipment on each run? Same Autoguider binning, barlow - the same image scales etc?
Something I've just bumped into -- my Kendrick dew heater settings have a bearing on my FWHM focus results! Until recently, I only ever saw 4s and 5s. Bumping Mr Kendrick down to 40% power, I now see high 1s and 2s. This no doubt would affect my PEC collection readings. I'll only measure PEC with Kendrick OFF from now on...
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