Table 3 Binding sites for Ramos T30 using separate models for replicates and taking the intersection (top) and the union (bottom) of regions identified by individual analyses at an 0.1% FDR (column 2), compared to a joint analysis of replicates at the same FDR (column 3)
From: Accounting for immunoprecipitation efficiencies in the statistical analysis of ChIP-seq data
Experiment | Identified using the intersection | Additionally identified | ||||
|---|---|---|---|---|---|---|
of separate models | using joint model | |||||
Number | Number | % | Number | Number | % | |
containing | containing | containing | containing | |||
TSS | TSS | TSS | TSS | |||
CBPT301 & CBPT302 | 5903 | 1444 | 24.46% | 9659 | 1942 | 20.11% |
p300T301 & p300T302 | 22984 | 5926 | 25.78% | 9861 | 2676 | 27.14% |
Identified using the union | Additionally identified | |||||
of separate models | using joint model | |||||
Number | Number | % | Number | Number | % | |
containing | containing | containing | containing | |||
TSS | TSS | TSS | TSS | |||
CBPT301 & CBPT302 | 22762 | 4601 | 20.21% | 18844 | 3870 | 20.54% |
p300T301 & p300T302 | 43003 | 10156 | 23.62% | 22765 | 1786 | 7.85% |