Hello, I am working on a set of Affymetrix wheat array, with some very ancient annotations included. I have been looking, and many sequenced organisms have a xxx.db annotation package that is used in conjunction with annotationDBi. I have found the wheatcdf, which seems to describe the environment (probe mapping), but this does not seem to be the same information as the xxx.db has. Is there such a package, or is wheat without such annotations? Thanks! Sam -- output of sessionInfo(): = -- Sent via the guest posting facility at bioconductor.org.

Hi Sam, On 6/12/2012 8:58 PM, Sam McInturf [guest] wrote: > Hello, > I am working on a set of Affymetrix wheat array, with some very ancient annotations included. I have been looking, and many sequenced organisms have a xxx.db annotation package that is used in conjunction with annotationDBi. I have found the wheatcdf, which seems to describe the environment (probe mapping), but this does not seem to be the same information as the xxx.db has. Is there such a package, or is wheat without such annotations? There is no such package. These packages depend on some fairly extensive infrastructure (they need an organism-level .db package, as well as an intermediate 'db0' package that Marc Carlson makes). Which packages have been supported is based on the cost/benefit where benefit is defined loosely as the number of end users who are likely to use the package. Unfortunately anopheles and yeast are the only plants to have jumped that hurdle so far. I checked the biomaRt package as well, and I don't see any support for Triticum there either. You could always just do something bootleg like downloading the annotations from Affy http://www.affymetrix.com/analysis/downloads/na32/ivt/wheat.na32.annot .csv.zip and parsing by hand. Best, Jim > > Thanks! > Sam > > -- 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