[BioC] Question about RINGO and follow up analysis

[Joern Toedling]

Hello,

please find a few answers below your questions.

On Thu, 21 Jan 2010 11:58:27 +0100, Dr. Viviana Menzel wrote
> 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?

The aim of the smoothing step is to down-weigh the individual reporter effects
which add noise to the reporter measurements of actual ChIP enrichment in the
respective genomic regions. I would recommend to perform this step to get more
accurate measurements of enrichment and estimates for the null distribution of
reporter intensities under non-enrichment.

> - which statistical analysis are adequate after finding ChIP-enriched
> regions?

That really depends on what you want to do with the enriched regions. For
example, you can relate the enriched regions to genes and then check whether
the list of affected genes is significantly associated to a biological theme,
as described in the GO or KEGG databases. The packages topGO or GOstats would
be useful for such an analysis.

> - there is any algorithm in Bioconductor similar/comparable to the 
> one use by Nimblegen for peaks finding (FDR calculation)?

Besides the peak-finding methods in Ringo, there are also peak-finding methods
in other packages, for example in ACME and BAC. One caveat may be that, with
histone modification, you would normally not expect the triangular peak shape
that is characteristic for transcription-factor peaks, so some of the methods
might be less useful for your data.

You can also have a look at this article in which I have described the
analysis of ChIP-chip with Ringo in a bit more detail than in the vignette.
http://www.ploscollections.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000227
The data package ccTutorial accompanies this article.

I am sure that other people from the list can provide you with additional
ideas how best to analyse your data.

Best regards,
Joern


---
Joern Toedling
Institut Curie -- U900
26 rue d'Ulm, 75005 Paris, FRANCE
Tel. +33 (0)156246927