Question: Cross validation error Admixture
0
gravatar for benhalimayossra
4.9 years ago by
Tunisia
benhalimayossra0 wrote:

Dear all,

 I'm using the ADMIXTURE’s cross-validation procedure i excuted this instruction 

# !/bin/sh

 for K in 3 4 5 6 7 8

do admixture --cv hapmap3.bed $K | tee log${K}.out

done

 my pruned data set were generated with plink software using this parameter (--indep-pairwaise 50 10 0.8) but when I checked with the values of CV error i found an unexpected increasing values.

Could you help me please

 

snp software error • 3.5k views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 4.9 years ago by benhalimayossra0

Do you have a reason to expect that you have more than 3 populations?

ADD REPLYlink written 4.9 years ago by Zev.Kronenberg11k

Yes, my reason is to compare the North African against the European populations and Middle East so here, I expect that I have more than 3 ethnicities

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by benhalimayossra0

Try K=2,3,4.  If three is the lowest than three is the best choice given the data and the model.  Another option is filtering out rare and high frequency variants.  

ADD REPLYlink modified 4.9 years ago • written 4.9 years ago by Zev.Kronenberg11k
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