Question: Cross validation error Admixture
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benhalimayossra • 0 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
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modified 16 months ago
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Biostar ♦♦ 20
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written
4.9 years ago by
benhalimayossra • 0
Do you have a reason to expect that you have more than 3 populations?
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
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.