[BioC] GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip

Christian Feller feller.christian at gmail.com
Wed Jul 9 13:31:56 CEST 2008

GC-sensitive normalization: naja, MAT läuft unter Python...

Und, die gestrigen Daten sind unterirdisch


-----Original Message-----
From: seandavi at gmail.com [mailto:seandavi at gmail.com] On Behalf Of Sean Davis
Sent: Wednesday, July 09, 2008 2:04 AM
To: Christian Feller
Cc: bioconductor at stat.math.ethz.ch; bourgon at ebi.ac.uk
Subject: Re: [BioC] GC-content sensitive normalization of Affymetrix tiling arrays for ChIP-chip

On Tue, Jul 8, 2008 at 6:58 PM, Christian Feller
<feller.christian at gmail.com> wrote:
> Dear Richard Bourgon and list,
> I am a newbie in analyzing ChIP-chip Affymetrix tiling arrays (GeneChip
> Drosophila Tiling 1.0R Array).
> My question is how can I take into accound the GC-effect of single probes if
> I do not have expression sets (due to the nature of a tiling array)? We had
> the idea of taking a fixed window size, defining the probes within them as a
> "probeset", and using GCRMA for background correction/normalization. In
> addition, can we use this configuration (normalization via GCRMA) for
> profiles with broad ChIP-enriched regions (as it is the case for many
> histone modifications).
> If there are some additional advice especially for the pre-processing steps
> I would be very happy!
> Until now, we do the normalization using vsn2.

Hi, Christian.  Do you have the input DNA from which you are going to
form a ratio, or are you attempting to do a single-channel analysis?
If the latter, then you might look at MAT from Shirley Liu's group.  I
don't think it is available for R, but the algorithm could probably be
coded in R relatively easily.  There are likely other solutions.


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