Not so much an R/BioC answer, but there are several programs out there for 
tiling analysis, one of which accounts for probe nt composition.
It is called MAT, by Shirley Liu's lab at Harvard.

I haven't used R for my stuff (Arabidopsis ChIP-chip on the tiling arrays) 
because there aren't library files yet (and I am not adept enough to make them)
[if someone reading this knows of their existence please let me know!]
So I have been using MAT, and another program TileMap.  Both show good 
correlation with ChIP-qPCR data.


Siobhan


At 03:58 PM 08/07/2008, Christian Feller 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.
>
>Thank you in advance!
>
>Best wishes,
>
>Christian Feller
>
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>
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S. A. Braybrook
Graduate Student, Harada Lab
Section of Plant Biology
University of California,  Davis
Davis, CA 95616
Ph 530.752.6980

The time is always right, to do what is right.
- Martin Luther King, Jr.  
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