hello! I'm working with the RJpGene.1.0 and RCnGene.1.0 arrays from Affy and I can't find the .CDF files, where could I find them? is there a way to create them? I only have the .CEL files. thanks! ayel??n -- output of sessionInfo(): . -- Sent via the guest posting facility at bioconductor.org.

Hi Ayelen, On 7/3/2013 2:40 PM, Ayelen [guest] wrote: > hello! > I'm working with the RJpGene.1.0 and RCnGene.1.0 arrays from Affy and I can't find the .CDF files, where could I find them? is there a way to create them? There are no cdf files for these arrays. Instead there are multiple files you will need. For each array you need: 1.) pgf, clf, mps files - these are included with the library files (e.g., http://www.affymetrix.com/Auth/analysis/downloads/lf/wt/RJpGene-1_0-st /RJpGene-1_0-st_rev01.zip for the Japanese rice). You have to unzip the file you download, and then start opening the subdirectories until you get to the very last one, and in there you will find these files. 2.) The annotation files (http://www.affymetrix.com/Auth/analysis/downloads/na33/wtgene-32_2 /RJpGene-1_0-st-v1.na33.2.irgsp1.transcript.csv.zip and http://www.affymetrix.com/Auth/analysis/downloads/na33/wtgene-32_2 /RJpGene-1_0-st-v1.na33.2.irgsp1.probeset.csv.zip for the Japanese rice). If you want to use the oligo package, collect all these files in a single directory, and then install pdInfoBuilder using biocLite (and oligo, for that matter). Then follow the instructions in this thread: https://stat.ethz.ch/pipermail/bioconductor/2013-March/051335.html You will of course need to substitute Rice and Oryza sativa for the organism and species. Let us know if you get stuck. Best, Jim > I only have the .CEL files. > > thanks! > ayel??n > > -- output of sessionInfo(): > > . > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099