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