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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