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 > > [[alternative HTML version deleted]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor 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. [[alternative HTML version deleted]]