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Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that?
If…
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![Here is the code I am using for the analysis][1]
[1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
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According to the link:
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obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
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Okay, that shows us the problem, but not what we need to solve it.
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In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1].
[1]: https://groups.goo…
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Yes, but I think the problem is what to do when MAF = 0.5
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In Plink, A1 is usually a minor allele and A2 a major allele.
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