Assessing key decisions for transcriptomic data integration in biochemical networks
Fig 2
Preprocessing decisions affect the definition of active reactions sets.
(A) Twenty different combinations of preprocessing decisions led to a large diversity number of reactions considered as active. (B) The first three principal components (PCs) explain most of the variance in the number of active reactions in a GEM. (C) Thresholding contributes the most to the first PC and more specifically the main contributor is the thresholding approach (i.e. local or global). (D, E and F). The influence of thresholding parameter selection is clear in the first PC (F), while the networks are less influenced by the gene mapping method (E) and the order of preprocessing steps used (D).