Fig. 14

Cluster 4 significant genes from the soybean iron metabolism data overlaid on a scatterplot matrix. Example of using a scatterplot matrix to assess DEG calls from a model in the iron-metabolism soybean dataset. There were 17 significant genes in Cluster 4 after performing a hierarchical clustering analysis with a cluster size of four (Fig. 2). These significant genes are overlaid in orange on the scatterplot matrix. For the most part, they do not seem to follow the expected patterns of differential expression: In many of the scatterplots between treatments, the orange points do not seem to deviate much from the x=y line. Moreover, in the scatterplots between P.1 and P.2 as well as P.1 and P.3, the orange points seems to indicate an underexpression of the P.1 replicate. We similarly saw somewhat messy looking DEG calls in Cluster 4 in the form of parallel coordinate plots (Fig. 2) and litre plots (Fig. 10g and h)