Hi all, I'm new to using R, and have been trying to figure out how to take some CEL files from an Affy U133A chip, RMA them, and combine probesets into entrez IDs. I've tried searching the bioconductor help lists but can't find an appropriate thread, though I'm sure this has been addressed many times, and couldn't find a proper "workflow" either. Any help is much appreciated! Brian. [[alternative HTML version deleted]]

Hello, I'm also new to this, but I maybe I can help you. This is a good lab that explains that in detail: http://www.bioconductor.org/help/course- materials/2006/biocintro_april/thurs/affy/Affy.pdf But basically I think you should try the "affy" package and the respective vignette (which is a king of hands on manual). > biocLite("affy") > library(affy) > openVignette() Should help you. Or else just try the direct link to the vignette: http://www.bioconductor.org/packages/2.7/bioc/vignettes/affy/inst/doc/ affy.pdf I hope I helped. Cheers On Wed, Feb 23, 2011 at 5:53 PM, Brian Tsai <btsai00@gmail.com> wrote: > Hi all, > > I'm new to using R, and have been trying to figure out how to take some CEL > files from an Affy U133A chip, RMA them, and combine probesets into entrez > IDs. I've tried searching the bioconductor help lists but can't find an > appropriate thread, though I'm sure this has been addressed many times, and > couldn't find a proper "workflow" either. > > Any help is much appreciated! > > Brian. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- João Moura [[alternative HTML version deleted]]

hello Brian, have you visited here - http://www.bioconductor.org/help/workflows/oligo-arrays/ best, amit m Graduate student IGIB, Delhi On Wed, Feb 23, 2011 at 10:23 PM, Brian Tsai <btsai00@gmail.com> wrote: > Hi all, > > I'm new to using R, and have been trying to figure out how to take some CEL > files from an Affy U133A chip, RMA them, and combine probesets into entrez > IDs. I've tried searching the bioconductor help lists but can't find an > appropriate thread, though I'm sure this has been addressed many times, and > couldn't find a proper "workflow" either. > > Any help is much appreciated! > > Brian. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]