Fig. 2

A selection of the default outputs from the Normalised Expression workflow, using the demonstration dataset. Three sample groups are presented—Lamina Propria (LP) (red), Mesenteric Lymph (ML) (green) and Mesenteric Lymph Node (MLN) (blue). a Density plots of the per sample distribution of expression values—across all genes. Expression is given on a log10 scale. b Principal component analysis (PCA) proportion of variance plot. The % of variation explained by each component is given on the Y-axis. c PC1 versus PC2 scatter plot. The % of variation explained by each component is given on the axis label. d Sample to sample correlation heatmap. Correlations were determined using all genes and a Spearman Correlation Coefficient (SCC). Colour indicates SCC with − 1 as the darkest blue and 1 as the darkest red. e Table of the 5 most highly expressed genes in MLN. Values indicate the mean expression of each gene in each of the three sample groups. f Gene expression violin plot with jitter values for each of the four most highly expressed genes in MLN. Black dots denote individual samples. The red dot and whisker denote mean and standard deviation respectively