Additional file 4 of Visualization methods for differential expression analysis

Scatterplot matrix for gene cluster that were added as liver-specific dEGs after tMM normalization. Scatterplot matrix of the 317 genes that were in the first cluster (of Fig. 20) from genes that were added as liver-specific DEGs after TMM normalization. With this scatterplot matrix, we see that the genes do not demonstrate the expected patterns of DEGs too strongly (they do not deviate much from the x=y line in the treatment scatterplots). In fact, these pink genes appear similarly to what we saw from the scatterplot matrix of the red genes (Additional file 3). This is somewhat of a surprise, given that the pink genes were added by TMM normalization, while the red genes were removed by TMM normalization. Stated differently, we would expect the pink genes to appear more like differentially expressed genes if TMM normalization is appropriate, but we could not confirm this expectation. We solved this problem using standardization techniques (Figs. 23 and 24).(JPG 135 kb)