Basic Analysis of NimbleGen ChIP-on-chip Data using Bioconductor/R (PROT43)

Hybridization of chromatin immuno-precipitation (ChIP) material to tiling arrays at NimbleGen service facilities usually leaves the customer with a set of data files that are of limited use. Most information about the experiment is gained by either displaying immunoprecipitate(IP)/input ratio tracks (the GFF files provided) of individual hybridisation experiments with NimbleGen?s SignalMap software or by scanning the list of peaks identified by the automated data analysis. Summary profiles from replicate experiments cannot be investigated; further calculations are left to the customers. Apart from the fact that data quality cannot be directly evaluated, raw data is not corrected for systematic signal distortions in the generation of ratio GFF files. Furthermore, the robustness of the provided peak finding procedures is questionable, as the algorithm will frequently identify many "significant" peaks in noise-only experiments.