Can 'annotate' package annotate microarray data other than affymetrix? And how? Thank you. Yihuan

>Can 'annotate' package annotate microarray data other than affymetrix? And >how? Thank you. The annotate package does annotation based on existing annotation packages. If there is an annotation package for your microarray, sure. If not, you will have to build one. Please have a look at the vignettes for AnnBuilder to learn how to build one yourself. > >Yihuan > >_______________________________________________ >Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor Jianhua Zhang Department of Biostatistics Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084

The annotate package does not annotate anything - it provides the software infrastructure that is common to all (many, most, ...) meta-data packages. Meta-data packagess are built by AnnBuilder. It mainly requires as input a file with two columns, one with the manufacturer IDS (those that are used on the chip) and another set of public ids (eg LocusLink, UniGene) etc. and from that you can construct annotation packages that look like the Affymetrix ones that we commonly build. We would build cDNA if we had access to a widely used set of mappings, but mostly cDNA are done locally in small numbers and it is not so useful to have them on a website for the whole world (to say nothing of the workload) Robert On Jan 5, 2005, at 11:52 AM, Yihuan Xu wrote: > Can 'annotate' package annotate microarray data other than affymetrix? > And > how? Thank you. > > Yihuan > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----------------+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: (206) 667-1319 | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center | | email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----------------+