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Saturday, August 20, 2011

MDS and PCA plots: for V157-V247

I have decided to publish MDS and PCA plots made (in PDF formats) for the latest run (see my previous post)

MDS plot
PCA plot


  1. I see only two Chuvash individuals and no Uzbek individuals on the PCA plot. Were they not included in the PCA analysis, or are they in a part of the PCA plot so remote that you didn't show that part of the PCA plot?

    Also, is it a PC3/PC4 PCA plot? If yes, where is the PC1/PC2?

  2. @Onur

    Chuvash and Uzbek individuals were intially included into Eigensoft input file. In Eigensoft option, I choosed 3 SDs for outlier removal:any individual with 3 standard deviation (3DS) along one of k top principal components > s would be removed as an outlier.

    I also plotted PC3 against PC4, because it appeared to be more informative.