Figure 3

Estrogen receptor status of FFPET samples: sequence detection sensitivity and specificity by different methods. Each point of a particular color in the plot represents the effect size (difference between mean expression in ER+ and ER– samples) found in FF samples and FFPET samples using a particular workflow. Different quadrants of the plot are marked so as to assist in classifying the findings. For example, false negative (FN) findings are those which are present in FF but absent in FFPET. Presence and absence is decided based on the observed effect size with the widely accepted threshold of 2-fold change (up or down). One particular case, referred to as a wrong positive finding (WP), not observed in our experiments, is when a relevant (>1 in absolute value) effect in FF stays relevant but changes its direction in FFPET.