removal of more PCs from the data, the degrees of freedom of the data will decrease. Furthermore, it is not immediately clear which PCs will actually capture physiological, environmental, and systematic variation, which might lead to removal of genetically determined expression variation as well. Therefore a tradeoff has to be made on the number of PCs to subtract from the data. We assessed this systematically, by removing up to 100 PCs from the genetical genomics dataset (in steps of 5).
