[BioC] Advice for ChIPchip-Analysis

Karin Zimmermann karin_z at gmx.de
Mon Jul 27 13:38:45 CEST 2009

> Betreff: Re: [BioC] Advice for ChIPchip-Analysis
> Hi Karin,
> please have a look at the vignettes of the package ccTutorial, which is a
> companion package to the PLoS Computational Biology article
> 'Analyzing ChIP-chip Data Using Bioconductor'.
> Especially the 'supplementary text' vignette may provide you with a few ideas
> for identifying differences in enriched regions between groups. One idea would
> be to look for overlaps between regions defined for group 1 and regions
> defined for group 2. For identifying overlaps, the package Ringo provides a
> function regionOverlap, but the packages genomeIntervals and IRanges contain
> more efficient functions for identifying overlapping genomic regions.
> For preprocessing the data, you could have a look the function
> normalizeByReference from package tilingArray.
> Best regards,
> Joern
> On Fri, 24 Jul 2009 11:03:45 +0200, Karin Zimmermann wrote
>> Hello all,
>> I have ChIP-chip and expression data for six different cell-lines. I
>> am new to ChIP-Chip analysis and would therefore need some advise to
>> analyse them correctly.
>> Our experimental setting is:
>> For each of the six celllines, three immuno-precipitated and three
>> non specific (IgG) chips (Affymetrix Promoter Tiling Array 1.0R)
>> have been spotted, resulting in 36 chips. The six celllines are
>> divided in two groups, for the sake of convenience I call them group
>> A and B. Our research group is interested in differences between the
>> two groups. So in patterns which differentiate the two groups. To be
>> precise, we are interested in genes which are significantly enriched
>> in group A but not B and vice versa.
>> What would be a good approach to perform such kind of analysis? The
>> publications concerning chIP-chip analysis (like MAT, Ringo, and
>> others) I've read sofar describe the data analysis to find chIP
>> enriched region. But I'm interested in regions/genes which are
>> differentially enriched between group A and group B.
>> Thanks in advance.
>> Karin
> ---
> Joern Toedling
> Institut Curie -- U900
> 26 rue d'Ulm, 75005 Paris, FRANCE
> Tel. +33 (0)156246926
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