Figure 1 Box-and-whisker plots (boxplots) of the expression values (normalized as TPMs) for each sample. Typically, it is expected that the boxes have similar positions and widths. If the distribution of a sample is very different from the others, this may indicate an experimental problem.
Figure 2 Barplot with the estimated expressed genes per sample. We assume a gene as expressed when it has at least one transcript sequenced per million of sequenced transcripts. Big differences on the number of expressed genes may indicate an experimental problem.
Figure 3 Heatmap of expression similarity between samples. It shows the distance between samples calculating the SERE coefficient between each pair of samples. Similar samples have lower values in the graph. Patterns in this plot can indicate clustering of the samples either because of intended biological or unintended experimental factors. Samples with experimental problems may have a high distance against the others.
Figure 4 PCA plot of samples. It shows a scatter plot of the samples along the first two principal components. The spatial arrangement of the points in the plot reflects the overall data (dis)similarity between the samples. It can be useful to explore the samples similarity and whether this is according to an intended experimental factor, or according to unintended causes such as experimental problems.