The standard workflow involved in applying SCEPTRE to a new dataset, using the Papalexi gene expression data as a running example. First, SCEPTRE is applied to analyze a set of automatically constructed negative control pairs (the calibration check). The resulting negative control p -values are plotted on a QQ plot to ensure uniformity (upper left), and the negative control log-fold changes are plotted on a histogram to ensure symmetry about zero (upper right). Second, SCEPTRE is applied to analyze the discovery pairs (the discovery analysis). The discovery p -values are superimposed over the negative control p -values to ensure that signal is present in the discovery set (lower left), and a volcano plot is created (lower right).
