Figure 14.

Finding true q-values. (a) Plot of the percentage of all probesets called 'differentially expressed' that are unbound probesets at various q-value cutoffs. (b) Mean log2 intensity versus mean log2 difference between C and S replicates for all probesets. Probesets are colored based on their classification. Empty probesets are grey, and those that can be mapped to a transcript are colored by fold change as indicated by the colored lines, which represent the true fold change of each classification. (c) Same plot as (b), but probesets are colored by q-values. Green symbols represent probesets with calculated q-values below 0.10, and red symbols represent probesets with q-values < 0.0003 (observed FDR of 10%).