Dinh 2011/NOTES/2011-8-29

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48 African Methylomes (UPenn)

  • PCA plots: on at ~50K Cpgs (no missing values) and at ~1.2K SNPs (also no missing values allowed)
  • Note: qc factor is very strongly correlated with genetic factors within this sample
  • Sarah mentioned that PC2 might be related to metabolism
  • Histogram of the Cpg rotations on PC2:
  • Used >=0.012 cut off to obtain the dominating Cpgs on PC2, obtained