hi all, we are probably going to use affymetrix tiling arrays for human. i have understood that in some ways it is possible to use gcrma for image preprocessing and that the quantile normalization might be a reasonable method. but i was wondering if there is (or if there is going to be) any ad hoc tool in bioconductor also for the later steps of the analysis and interpretations of such experiments. any suggestions are warmly appreciated. thanks, greetings d -- Dario Greco Institute of Biotechnology - University of Helsinki Building Cultivator II P.O.Box 56 Viikinkaari 4 FIN-00014 Finland Office: +358 9 191 58951 Fax: +358 9 191 58952 Mobile: +358 44 023 5780 Lab WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/ Personal WebPage: http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm

Hi Dario, Have a look at the tilingArray package. It's description says: The package provides a function for DNA reference normalization of probe effects, a fast model-based segmentation algorithm, and a nice along-chromosome visualization of the segmented data. Data structures and user interfaces are under development are subject to change. Best, Steffen > hi all, > we are probably going to use affymetrix tiling arrays for human. > i have understood that in some ways it is possible to use gcrma for image > preprocessing and that the quantile normalization might be a reasonable > method. > but i was wondering if there is (or if there is going to be) any ad hoc > tool > in bioconductor also for the later steps of the analysis and > interpretations > of such experiments. > any suggestions are warmly appreciated. > thanks, > > greetings > d > > -- > > Dario Greco > > Institute of Biotechnology - University of Helsinki > Building Cultivator II > P.O.Box 56 Viikinkaari 4 > FIN-00014 Finland > > Office: +358 9 191 58951 > Fax: +358 9 191 58952 > Mobile: +358 44 023 5780 > > Lab WebPage: > http://www.biocenter.helsinki.fi/bi/dna-microarray/ > > Personal WebPage: > http://www.biocenter.helsinki.fi/bi/dna-microarray/dario.htm > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >