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 -- Jetzt kostenlos herunterladen: Internet Explorer 8 und Mozilla Firefox 3 - sicherer, schneller und einfacher! http://portal.gmx.net/de/go/atbrowser

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

> 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 > > -- GRATIS f?r alle GMX-Mitglieder: Die maxdome Movie-FLAT!