Question: Should replicate analyses of ADMIXTURE all have the same cross-validation values
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gravatar for devenvyas
3.5 years ago by
devenvyas580
Stony Brook
devenvyas580 wrote:

This is a pretty simple question. I have noticed when I run my ADMIXTURE values for K=2 to 20 with ten replicates, my output CV values for each value of K are always identical for all 10 replicates. I've seen literature where there is some variation in replicate CVs. They do have different loglikelihoods, but the CVs fall out the same.

I was wondering, is this normal?


 

admixture • 1.3k views
ADD COMMENTlink modified 2.1 years ago by Santiago Montero-Mendieta120 • written 3.5 years ago by devenvyas580
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gravatar for Brice Sarver
3.5 years ago by
Brice Sarver2.6k
United States
Brice Sarver2.6k wrote:

I've seen this with my ADMIXTURE runs in the past. For what it's worth, I've noticed more variation in the likelihoods of STRUCTURE runs, meaning that there can be a bit of a difference among sets of replicates when selecting an 'optimal' K (whatever that means). That's not using cross validation, though.

ADD COMMENTlink written 3.5 years ago by Brice Sarver2.6k
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gravatar for Santiago Montero-Mendieta
2.1 years ago by
Sweden

I have also noticed identical CV-error values for every replicate ADMIXTURE run. This is due to the initial seed number that is always 43. There is an option of generating a pseudo-random seed using the system clock (flag -s). Here is how I ran it:

admixture -s time --cv file.ped K -jN
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by Santiago Montero-Mendieta120
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