A measurement of euclidean distance, however here we are observing the difference based on color. The darker the color the closer the data is to one another and vice versa. This means that the SAM samples are most similar to the SAM samples and the Leaf samples are most similar to the Leaf samples. Also, since the SAM samples are darker than the Leaf samples this means that the SAM samples are more similar to one another thanthe Leaf samples are to one another (which further supports the data from the figure above),

Blue= genes that are downregulated (to our control our test samples have less counts of transcripts)

Description: As the mean of normalized counts increases then the red line should get lower (take a J shape). This means that this set of data is showing what we expect it to.

Histogram of the p-value for each gene being compared. See a higher significance in over 14,000 genes that are likely under the 0.05 threshold. This is an unadjusted p-value histogram, adjusting these p-values would be beneficial to see more conservative p-values (less than 14,000, which would show us what is changing the most between these groups). Taking the extra step to adjust these p-values is recommended.

As we move across the x-axis the number of transcripts changes and we start to see smaller fold changes. More counts - blue dots are coming in and smaller differences are going to be more significant.