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Average overlap frequency/ staining index

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marthabrainard1

Participant

Posts: 14

Joined: Wed Aug 25, 2021 2:10 pm

Post Thu Feb 17, 2022 10:47 pm

Average overlap frequency/ staining index

Hi CyTOFers,

Does anyone have any suggestions on how to calculate a staining index for mass cytometry data without using R? I skimmed the following paper about average overlap frequency, but my computer can't handle running the packages (even if I knew how to use them efficiently...) https://www.sciencedirect.com/science/a ... via%3Dihub

Thank you!
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tomash

Contributor

Posts: 22

Joined: Sun Oct 19, 2014 10:15 pm

Post Thu Feb 17, 2022 11:46 pm

Re: Average overlap frequency/ staining index

If you are using FlowJo or any other analysis software you should be able to export the relevant median and SD/rSD data for the positive and negative populations from each of your single stained samples, and do the calculations in excel or similar? The equations are fairly straight forward, it's just a matter of getting the right numbers out of the program.

It can be a bit fiddly, as you have to generate the statistic for the relevant parameter (e.g. MFI for 165Ho) on the relevant single-cell stain (the one stained with a 165Ho-antibody) separately. Alternatively you could generate measurements of all channels on all single-cell stain controls -- this would be faster to get the numbers out, but might take longer to sort through when doing your calculations.

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