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

[Sean Davis]

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.

Sean