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I'm having problems with data analysis here.

I have flow cytometry data being collected on a Fortessa, and when I import them into FlowJo 8.7, all of my fluorescence values are systematically 10X lower than they are on the cytometer. No idea what's going on here, anybody can help? If you want screenshots and photos of the data, I'm happy to post them up.

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  • $\begingroup$ What is your fluorescent output? $\endgroup$ – bobthejoe Oct 14 '12 at 9:00
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I have this issue too with data from a Partec PAS III. I don't consider it a problem, as it's really just the x-axis which is one order of magnitude higher. At the end, all values coming from the machine are arbitrary values, so as long as the change is systematic, there's no problem.

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The answer I have come to is the difference between FCS2.0 and FCS3.0 files. The binning pattern is different, and as such FCS2.0 files arbitrarily lowered my flow cytometry values compared to what I saw on the FACS DiVa software.

In the end, exporting with FCS3.0 was the way to go. If your software supports this, I'd highly recommend doing so!

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