PCA and CCA reveals population structure.

(A) A PCCA projection of the batch-corrected expression matrix that shows that expression reflects population structure. While the individuals, labeled according to their population, do not cluster as clearly as with genotype data (Fig 1B), there is clear population structure in the PCCA projection of the batch-corrected expression data. (B) A leave-one-out cross-validation experiment showing that individuals are approximately projected to their populations of origin even when the projection matrix is learned without their expression or genotype data. The mean re-construction errors in (A) the left-in samples and (B) the held-out samples are similar and overlayed on top of the Figure. The first two canonical correlations are 0.963 and 0.766.