PCA plots at the probe set level show two main sources of variation among the 20 samples. The first principal component explains 65% of the variance and corresponds, as expected, to the biological source of the sample: brain (B) vs. reference (R). The second principal component explains 20% of the variance and corresponds to the "lab effect" between VT (blue), and McGill (red) – that is, it illustrates the technical variability across labs.
Bemmo et al. BMC Genomics 2008 9:529 doi:10.1186/1471-2164-9-529