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Hello Joseph, Which array are you using?? First you need to create a CDF for your affymetrix tiling. For that you need the makeplatformdesign package. You also have to take from Affymetrix the BPMAP and CIF files available for your tiling array. ***** R Code **** > library(makePlatformDesign) > makePDpackage("AFFY_TILING.bpmap",file1="AFFY_TILING.cif", manufacturer="affymetrix", type="tiling") Then you check and build the package you obtained (in unix: with "R CMD check AFFY_TILINGcdf" and "R CMD build AFFY_TILINGcdf") The name of the cdf (I put here as example AFFY_TILINGcdf) will be given by makePDpackage command. Then you have a cdf for your tiling :) You can read your cel files with oligo package: >library(oligo) >library(AFFY_TILINGcdf) data=read.celfiles(list.celfiles(),pk="AFFY_TILINGcdf") Here you have access to all the data available on the tiling array. Then, depending on the analysis you want to do, you will need to map the probes on the array to genes or something else... Regards, Naira joseph wrote: > Hello > The vignette "An Introduction to the Oligo Package" addresses only Affymetrix SNP Arrays. Does any one have an example of how to analyze Affy tiling arrays with oligo and is willing to share it? > Thanks > Joseph Dhahbi > CHORI > > > > ______________________________________________________________ ______________________ > Never miss a thing. Make Yahoo your home page. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- ================================================================== Naira Naouar Tel:+32 (0)9 331 38 63 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM nanao at psb.ugent.be http://www.psb.ugent.be

Hi Benilton, All my code is present below on the forwarded message. Thx a lot, Naira -------------- next part -------------- An embedded message was scrubbed... From: Naira Naouar <nanao@psb.ugent.be> Subject: Re: [Fwd: [BioC] Oligo package and tiling arrays - PM and MM] Date: Wed, 05 Dec 2007 16:01:26 +0100 Size: 5237 Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071213/ bf08bdf2/attachment.mht