Figure 4.

Intersector and ChipStat performance. (a) The number of probe sets shown to increase from 2 to 5 weeks of murine mammary gland development was tabulated as a function of the number of probe sets expected to increase by chance, and a comparison of ChipStat (p_ps = 0.05), Intersector (MAS 5.0 change calls), and Intersector (MAS 4.0 change calls) is shown. (b) Venn diagram showing distinct probe sets identified by ChipStat and Intersector. The number of genes shown to be differentially expressed at the indicated expected false-positive levels is shown for ChipStat (CS) (p_ps = 0.04), Intersector (IT) with MAS 5.0 calls, and Intersector (IT) with MAS 4.0 calls. (c) False-positive rates for ChipStat (CS 6/16: p_ps = 0.05, 6/16 probe pairs increasing; CS 9/16: p_ps = 0.05, 9/16 probe pairs increasing), Intersector (MAS5) (IT 7/9: 7/9 increases or marginal increases; IT 8/9: 8/9 increases or marginal increases), or ChipStat and Intersector together (Combined: intersection of CS 6/16 and IT 7/9) are shown. (d) Combined performance of ChipStat and Intersector. Increases from 2 to 5 weeks of mammary gland development are shown for ChipStat alone (p_ps = 0.05), Intersector alone (MAS 5.0), and optimized intersections of ChipStat and Intersector (see Additional data file 1).