[BioC] Advice for ChIPchip-Analysis

Joern Toedling Joern.Toedling at curie.fr
Fri Jul 24 13:30:53 CEST 2009

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,

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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