Fig. 13

Data transformation and normalization with edgeR R library and differentially expressed gene analysis results. a Boxplot of expression difference among six samples. Figures were presented as raw data (Count), Log 2 (counts per Million reads + 1), and TMM Normalization values. A visual representation of a box plot with percentiles (median, 25%, 75%, maximum, and minimum values). b density plot of expression difference among six samples. Raw data (Count), Log 2 (counts per million reads + 1), TMM Normalization values. c Number of significant contigs by fold change and p value. d Log2-fold change and p value obtained from the comparison between two groups plotted as a volcano plot. e A smear plot to show an expression difference in cells between the control and fungal elicitor-treated groups according to the overall average expression level (Smear). (x-axis: average log CPM, y-axis: log2 fold change)