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In the scientific paper "Mapping the Antigenic and Genetic Evolution of Influenza Virus's" Supporting Material, Smith et al write about determining antigenic distance Dij. However, I don't understand how one could calculate Dij from HI values of <10. Is it better to remove these data values or to change it to 9?

Also, regarding the missing data, how does one make a comprehensive antigenic map using shape space distance dij? I see that an error function must be minimized, but how does that give dij for all the missing data? Should missing data be ignored for the error function?

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  • $\begingroup$ I don't know how Derek's group handles it (don't have time to look now) but conventionally HI assays less than 10 are called "9" for statistical purposes, and I assume that's how they did it. Have you looked at Henry Wan's antigenic distance web site (sysbio.cvm.msstate.edu/software/AntigenMap/about)? I think he talks more about his approach $\endgroup$
    – iayork
    Feb 19, 2019 at 14:06
  • $\begingroup$ You're clearly serious about this project, but asking on se.biology isn't the best problem-solving approach for this kind of in-depth question. Can you find a mentor in the field who can work with you specifically? $\endgroup$
    – iayork
    Feb 19, 2019 at 14:36
  • $\begingroup$ Thank you @iayork. I am a high school student and I am working on this project for a research competition. I appreciate your answering my questions for the past few months. $\endgroup$
    – FIREREED
    Feb 21, 2019 at 4:08
  • $\begingroup$ I'd like to help more, but this isn't my speciality, not to mention that I have my own group to run. Since you have good, specific and focused questions, you could just try writing to Derek Smith, who is a very friendly guy. Trever Bedford is enthusiastic and committed to open-source software and has a strong Twitter presence, and you might get answers from him too. Jesse Bloom is very knowledgeable and has open-source projects. $\endgroup$
    – iayork
    Feb 21, 2019 at 11:23
  • $\begingroup$ Alright, thank you @iayork. I will contact the people whose names you mentioned. $\endgroup$
    – FIREREED
    Feb 23, 2019 at 15:43

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