[BioC] Question about RINGO and follow up analysis

Dr. Viviana Menzel vivianamenzel at gmx.de
Thu Jan 21 11:58:27 CET 2010


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
- 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

Dr. Viviana Menzel
Rottweg 34
35428 Langgöns
Tel.: +49 6403 7748550
Mobil: +49 177 5126092
E-Mail: vivianamenzel at gmx.de
Web: www.dres-menzel.de

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