Figure 2
From: Estimation and correction of non-specific binding in a large-scale spike-in experiment
Plot of mean log2 difference versus mean log2 intensity (MA plot) showing FPs. MA plots are for probes normalized with the GoldenSpike method using (a) all null probesets (empty and FC = 1) as a subset and (b) only FC = 1 probesets as a subset. In the plots, red spots represent FC > 1 probesets that are called significantly differentially expressed (q < 0.1) by the modified Cyber-T method suggested by Choe et al. (that is, TPs). Pink spots represent FC > 1 false negatives. Grey symbols represent empty probesets that are not called significantly differentially expressed (true negatives), and blue symbols represent empty probesets that are called significantly differentially expressed (FPs). Black symbols represent FC = 1 true negatives, and green symbols represent FC = 1 FPs.