Dear Bioconductors, I've found the page http://bioconductor.org/data/metaData.html which has source packages for drosophila2cdf and drosophila2probe, but I can't find the source for drosophila2 itself. Is this supposed to live at this page or is there some other canonical place where I can find this? Thanks in advance, Cyrus

If you are looking for the annotation package for the drosophila2 chip, it hasn't been done. It could possibly be done using AnnBuilder, but you may have to do some modifications to the code in ABPkgBuilder() in order to correctly retrieve the annotation information. Note that Affymetrix has a .csv file on their website that contains all the annotation information that they have about the genes on this chip. In addition, you may be able to use the biomaRt package to get annotation information (not sure, I haven't used it yet). Best, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> Cyrus Harmon <ch-bioc@bobobeach.com> 04/08/05 7:10 PM >>> Dear Bioconductors, I've found the page http://bioconductor.org/data/metaData.html which has source packages for drosophila2cdf and drosophila2probe, but I can't find the source for drosophila2 itself. Is this supposed to live at this page or is there some other canonical place where I can find this? Thanks in advance, Cyrus _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.

Hmm... I was able to ape a working URL for the drosophila2 package, which is maintained by Chenwei Lin at FCHRC. I think it's a case of a missing URL on the metadata page. Or perhaps there's an "official" annotation package (via AnnBuilder) that does not yet exist. The package that I found has the drosophila2XXX mappings I was looking for, but clearly there's room for further access to fly annotations in bioconductor. Has anyone put together a flybase package yet? In particular, I'd like to see the mapping between gene symbols and flybase identifiers. If it hasn't been done yet, I'd be happy to look into pulling this together. Thanks, Cyrus On Apr 9, 2005, at 6:12 AM, James MacDonald wrote: > If you are looking for the annotation package for the drosophila2 chip, > it hasn't been done. It could possibly be done using AnnBuilder, but > you > may have to do some modifications to the code in ABPkgBuilder() in > order > to correctly retrieve the annotation information. > > Note that Affymetrix has a .csv file on their website that contains all > the annotation information that they have about the genes on this chip. > In addition, you may be able to use the biomaRt package to get > annotation information (not sure, I haven't used it yet). > > Best, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 >>>> Cyrus Harmon <ch-bioc@bobobeach.com> 04/08/05 7:10 PM >>> > Dear Bioconductors, > > I've found the page http://bioconductor.org/data/metaData.html which > has source packages for drosophila2cdf and drosophila2probe, but I > can't find the source for drosophila2 itself. Is this supposed to live > at this page or is there some other canonical place where I can find > this? > > Thanks in advance, > > Cyrus > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should > not be used for urgent or sensitive issues.