Consistency Analysis of Redundant Probe Sets on Affymetrix Three-Prime Expression Arrays and Applications to Differential mRNA Processing
Figure 3
Significance consistency among the redundant probe sets changes depends on FDR threshold.
A consistency index was computed for each gene with redundant probe sets at different FDR level. AG and GG indicate the original Affymetrix grouping and proposed genome-based groupings, respectively. AGP and GGP represent the AG and GG groupings. AGP and GGP refer to AG and GG groupings in which only probe sets called as “present” were included in the calculation.