Illustrative example of a technical confounding effect

The figure below shows PCA plots for an animal experiment with the LHS showing controls (1, black circles), infected animals (2, red triangles) and QC injections (green crosses). The RHS plot has been relabelled by cage and clearly shows clustering dependent on which cage each animal was housed in (0, black circles: QC injections; 1 to 4: cages 1 to 4).