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Thread: PCA plot using FLashpca

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    PCA plot using FLashpca

    Dienekes made a thread about this below:
    http://dienekes.blogspot.com/2014/01...rge-scale.html

    I decided to give it a test, and I must say it is a very fast software.
    I used R to generate the attached PCA plot. So mainly South Asian/Central Asian populations.
    Overall, this was as expected. Not sure why the Pulliyars are forming their own cluster. It could be a mislabeling.
    P.S. The Metspalu dataset has some mislabeling. For example, I think Tamil Nadu scheduled castes may be mislabeld.
    Attached Images Attached Images
    Last edited by everest59; 02-05-2014 at 12:38 AM.

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    I decided to clean up the PCA plot above a little bit. There are still some outliers (must be some mislabeling). I decided to add Singapore Indians to the plot above.
    See attached.
    Attached Images Attached Images

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    Excellent! everest59, could you try a global PCA with this? Also, could you try one with both of us on it? Thanks!

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    Sure. Btw Stein, you are in there. You and your mom have been labeled Pathan2. I am labeled Nepali.
    Sure, I will add 12 more populations to the pca above. Is that good enough?

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    Thanks everest! And sure, whatever you think would be good in terms of experimentation. Just out of curiosity, would you by any chance know the ID's of the two Pashtun samples which are close to me? Thanks again!

    Edit: Another question, but in your opinion, is this approach as good as regular PCA?
    Last edited by Sein; 02-05-2014 at 12:30 PM. Reason: Added an extra question.

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    Everest, could you add me as well? Curious how close I would be to you (Nepali) on this
    Paternal - Y-DNA: J2b2* (J-M241) Z2432+ Z2433+ Y978+ (J2b2a2b1*) (Hidden Content ) (YFull: YF02959) (FTDNA Kit B6225), mtDNA: M18a* (FTDNA Kit 329180) (YFull: YF63773)
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    Quote Originally Posted by everest59 View Post
    Sure. Btw Stein, you are in there. You and your mom have been labeled Pathan2. I am labeled Nepali.
    Sure, I will add 12 more populations to the pca above. Is that good enough?

    Add me as well mate? Thanks. At least to the first one?
    Last edited by Sapporo; 02-05-2014 at 01:19 PM.

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    Quote Originally Posted by Sein View Post
    Thanks everest! And sure, whatever you think would be good in terms of experimentation. Just out of curiosity, would you by any chance know the ID's of the two Pashtun samples which are close to me? Thanks again!

    Edit: Another question, but in your opinion, is this approach as good as regular PCA?
    Well, I can only figure out the IDs by adding texts. The texts appear jumbled up, but it appears that the one above you is 6af, whereas the one to the left of you is either 22af or 20af. I can't tell properly. All I see is af.
    Edit: Okay, I'm not sure if 6af is that close to you. She seems to the most North-shifted Pashtun.

    - - - Updated - - -

    Sapporo and Mcninja, email me your data and I'll add you to the pca plot above.
    Let me know if anybody else wants to be added.
    I'd like to add the Mal'ta specimen pretty soon as well, perhaps to global pca.
    Last edited by everest59; 02-05-2014 at 02:19 PM.

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    Quote Originally Posted by everest59 View Post
    Well, I can only figure out the IDs by adding texts. The texts appear jumbled up, but it appears that the one above you is 6af, whereas the one to the left of you is either 22af or 20af. I can't tell properly. All I see is af.

    - - - Updated - - -

    Sapporo and Mcninja, email me your data and I'll add you to the pca plot above.
    Let me know if anybody else wants to be added.
    I'd like to add the Mal'ta specimen pretty soon as well, perhaps to global pca.
    Thanks everest59! As a special request, is it possible for you to eventually create a PCA plot similar to the one I've attached? The PCA plot in question is basically only Eurasian populations. No Africans, North Africans, Amerindians, or Australasians-Oceanians. Just European, West Asian, Caucasus, South Asian, Central Asian, and East Asian-Siberian-Southeast Asian populations, minus all African or African admixed groups, and populations from the Americas and Oceania (sorry if that sounded repetitive). It would be interesting to compare to the Cristofaro PCA.

    journal.pone.0076748.g003.jpg

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    Quote Originally Posted by Sein View Post
    Thanks everest59! As a special request, is it possible for you to eventually create a PCA plot similar to the one I've attached? The PCA plot in question is basically only Eurasian populations. No Africans, North Africans, Amerindians, or Australasians-Oceanians. Just European, West Asian, Caucasus, South Asian, Central Asian, and East Asian-Siberian-Southeast Asian populations, minus all African or African admixed groups, and populations from the Americas and Oceania (sorry if that sounded repetitive). It would be interesting to compare to the Cristofaro PCA.

    journal.pone.0076748.g003.jpg
    Sure, I'll do that. I'll wait for Sapporo's and Mcninja's data first. Should be pretty easy.

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