Question: Should replicate analyses of ADMIXTURE all have the same cross-validation values
1
gravatar for devenvyas
4.0 years ago by
devenvyas610
Stony Brook
devenvyas610 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 • 1.5k views
ADD COMMENTlink modified 2.6 years ago by Santiago Montero-Mendieta130 • written 4.0 years ago by devenvyas610
1
gravatar for Santiago Montero-Mendieta
2.6 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 2.6 years ago • written 2.6 years ago by Santiago Montero-Mendieta130
0
gravatar for Brice Sarver
4.0 years ago by
Brice Sarver3.3k
United States
Brice Sarver3.3k 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 4.0 years ago by Brice Sarver3.3k
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