Fig. 23.

Standardized scatterplot matrix for gene cluster that were removed from kidney-specific DEGs after TMM normalization. Scatterplot matrix of the standardized 529 genes that were in the first cluster (Fig. 19) from genes that no longer remained as kidney-specific DEGs after TMM normalization. Even though the standardization process removes the interesting geometrical features we would otherwise see, it amplifies DEG patterns in meaninful ways. Namely, the genes of interest are now spread out more, and the replicate and treatment scatterplots are almost indistinguishable from each other, with both of them showing genes of interest crossing both sides of the x=y line. In other words, standardization of the data provides clear visualization evidence that TMM normalization was justified in removing these genes from DEG designation