Statistical comparison tracks

The Differential Expression for RNA-Seq tool will output one or more statistical comparison tracks.

An example of a statistical comparison track is shown in figure 29.28. Statistical comparison tracks make it possible to show differential expression data alongside other kinds of tracks in a genomic context.

Image statistical_comparison_track
Figure 29.28: Statistical comparison track view.

In particular, the Fold Change value will tell you how expression levels in group 2 are relative to that in group 1.

Note that it is not possible to derive these fold changes from the CPM values by simple algebraic calculations as the Differential Expression for RNA-Seq tool works by fitting a statistical model (which accounts for differences in sequencing-depth) to raw counts. Keep also in mind that p-values smaller than 10e-16 will be reported as equal to zero, and as a consequence these values will not appear on the volcano plot.

The track layout of the statistical comparison track can be customized as follows:

The expression track table view has three button.