Question: Perplexing ADMIXTURE results - one component present at K =10 disappears at 11, reappears at 12
0
gravatar for devenvyas
3.6 years ago by
devenvyas580
Stony Brook
devenvyas580 wrote:

Hello,

I looking at some ADMIXTURE analyses on human SNP data from the Affymetrix Human Origins array, and I am having a component disappear at K=11 and then re-appear at K=12. I have at least 10 replicates for every value of K for values 2 through 20.

CV error (K=1) 0.43206
CV error (K=2) 0.38759
CV error (K=3) 0.38116
CV error (K=4) 0.38019
CV error (K=5) 0.37783
CV error (K=6) 0.37654
CV error (K=7) 0.37589
CV error (K=8) 0.37577
CV error (K=9) 0.37559
CV error (K=10) 0.37556
CV error (K=11) 0.3762
CV error (K=12) 0.37605
CV error (K=13) 0.37639
CV error (K=14) 0.37705
CV error (K=15) 0.37766
 

I am looking K = 10, 11, and 12. While K=10 has the lowest CV error, a component of relevance to me doesn't show up until K=11. I've noticed that at K=10 (and lower too I believe), I have a component maximized in the Mbuti; however, at K=11 this component disappears and the Mbuti have proportions of different sub-Saharan African components and I have two new components arising (one maximized in the Mozabites and one in the Hazara). Then at K=12 the Mbuti component comes back and stays for good. This occurs across all replicates.

Has anyone else had similar ADMIXTURE results?

 

 

 

 

snp admixture • 1.1k views
ADD COMMENTlink written 3.6 years ago by devenvyas580

Have you pruned linked sites?

ADD REPLYlink written 3.6 years ago by Zev.Kronenberg11k

Yup, I pruned the dataset (--indep-pairwise 200 25 0.4) based on the publication my comparative data came from. After posting this I was looking at a paper from some of my advisor's collaborators, and I saw similar things (http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004393 see figure S1 and look at Biaka from K=15-18 or Karretjie from 14-16).

ADD REPLYlink written 3.6 years ago by devenvyas580
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1797 users visited in the last hour