[BioC] Question about RINGO and follow up analysis

[Dr. Viviana Menzel]

Hello,

I'm new in the analysis of ChIP-chip data, and have some questions.
My data: ChIP-chip dataset on post-translational modification of the
histone protein H4 (acetylation on K12) in human sperm. Microarray
platform: NimbleGen  promoter design, 385K two-array set.
I use the Ringo package to analyse the raw data. My questions:
- it is possible to find ChIP-enriched regions without smoothing the
reporter intensities?
- which statistical analysis are adequate after finding ChIP-enriched
regions?
- there is any algorithm in Bioconductor similar/comparable to the one
use by Nimblegen for peaks finding (FDR calculation)?

I will very appreciate some advices.

Thanks on advance

Dr. Viviana Menzel
Germany


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Dr. Viviana Menzel
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