Choosing projection values for a 2D SFS

[Aidan Short]

Hi Prof. Gutenkunst,

This isn't really an issue, but kind of a general question about choosing projection values. In the past I have tried to maximize the number of segregating sites based on the segregating SNPs in the two populations.
For example:
fs = dadi.Spectrum.from_data_dict(dd, ['population 1', 'population 2'], [100,50])

print(fs.S())

However, I noticed that tools such as easySFS suggest selecting the projection values based on the segregating SNPs in each of the single populations. 
For example: 

fs = dadi.Spectrum.from_data_dict(dd, ['population 1'], [100])

print(fs.S())

fs = dadi.Spectrum.from_data_dict(dd, ['population 2'], [50])

print(fs.S())

I guess I am wondering if it would be better for me to maximize the number of segregating sites within each population or between the two populations.

Sorry if this confusing, I am still new to using dadi.

Sincerely, 

Aidan Short

[Ryan Gutenkunst]

Hello Aidan,

In our own analyses, we tend to maximize the segregating sites across the whole spectrum. But to my knowledge no one has rigorously tested this rule of thumb. So do whichever seems more logical to you; I doubt it makes a big difference in any reasonable case.

Best,
Ryan

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[Aidan Short]

Thanks Ryan! I appreciate your advice!

Sincerely,
Aidan

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