Figure 3

Power calculations of absent call-only probe sets shows variable rates of false positives. Shown is the output of HCE-power [20] for five probe set algorithms, including two newer "hybrid" algorithms (PLIER, GC-RMA), expressed as a % of probe sets fulfilling specific criteria (β = 0.2, α = 0.05, effect size = 1.5 fold change). Muscle biopsies from 16 normal controls, and 10 Duchenne muscular dystrophy patients were used on U133A microarrays [27], and the 8,200 probe sets that showed an "absent call" by MAS5.0 algorithm on all 26 arrays were then loaded into HCE-power. These "absent calls" reflect poorly performing probe sets, where there is low confidence that signal specific to the transcript is detected above background levels. By this analysis, both RMA and GC-RMA show significant powering of 70–80% of these "absent call" probe sets with only 2 microarrays per group. This can be interpreted as a high proportion of false positive results expected from this project using RMA or GC-RMA. On the other hand, PLIER shows insufficient powering for 98% of the 8,200 probe sets, even at group sizes of 10 arrays/group. This suggests that PLIER will show no false positives.