Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
The interesting samples here are Gujarati (HRP0071), Bengali Brahmin (HRP0077) and Brazilian (HRP0074).
If you can't see the interactive bar chart above, here's a static image.
PS. This was run using Admixture version 1.04.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
If you can't see the interactive bar chart above, here's a static image.
I dare you to generalize!
PS. This was run using Admixture version 1.04.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
The interesting samples here are the Gujarati and the Punjabi. HRP0064 is very different from the other Punjabis so far.
If you can't see the interactive bar chart above, here's a static image.
PS. This was run using Admixture version 1.04.
While my computer's busy running K=12 admixture on batch 7, K=17 admixture on batch 1, some MClust experiments and converting 1000genomes data from vcf to ped and I am reeling from the pollen count (3,939 yesterday), here are some links to my personal genetics blogging.
For the record, my daughter complains about all the "Trantor windows" open on the computer all the time. She calls the terminal windows "Trantor" because of the shell prompt. My desktop is named Trantor. Now who can guess what my laptop, my other desktop and my wireless network are named?
Admixture lets you choose the number of ancestral populations, K. This number is really important and in a lot of cases we do not know how many ancestral populations our samples have descended from. In the Admixture manual, we are advised:
Use ADMIXTURE's cross-validation procedure. A good value of K will exhibit a low cross-validation error compared to other K values. Cross-validation is enabled by simply adding the --cv flag to the ADMIXTURE command line. In this default setting, the cross-validation procedure will do 10 repetitions, each time holding out 10% of the genotypes at
random.
I like this idea compared to using the BIC (Bayes Information Criterion) but I am plotting all the different variables for various K below.
For our Reference I dataset which is what I have used for most of the analysis so far, here is the spreadsheet for Log Likelihood, BIC, AIC and CV (cross-validation error). The plots follow.
Using the cross-validation error, the optimum value of K so far is 17 which is the largest I have run so far. It now takes days to run admixture (with cross-validation). Cross-validation almost doubles the time required to run.
For Reference II, here are the spreadsheet and graphs.
The cross-validation error is lowest at K=16 which is the highest I have run. So it is likely to decrease further for higher K.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
If you can't see the interactive bar chart above, here's a static image.
Look at how different the two Gujaratis are. Also, the Iraqi Kurd is more like our Iranian participants than the two Iraqi Arab participants.
PS. This was run using Admixture version 1.04.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
The interesting samples here are the Gujaratis and the Kurd.
If you can't see the interactive bar chart above, here's a static image.
PS. This was run using Admixture version 1.04.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
If you can't see the interactive bar chart above, here's a static image.
PS. This was run using Admixture version 1.04.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
The interesting samples here are the two Iraqi Arabs (HRP0042 & HRP0043) who have some African admixture.
If you can't see the interactive bar chart above, here's a static image.
PS. This was run using Admixture version 1.04.
Here are their ethnic backgrounds and the results spreadsheet. Also relevant are the reference I admixture results.
The interesting samples here are the two Iraqi Arabs (HRP0042 & HRP0043) who have some African admixture.
Also, we finally have a couple of Bengalis (HRP0049 & HRP0050) who have 13% East Asian for this run which is less than Razib's (HRP0002) and his parents' 19-20% but still higher than others.
If you can't see the interactive bar chart above, here's a static image.
PS. This was run using Admixture version 1.04.
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