[BioC] drosophila2 source question

Cyrus Harmon ch-bioc at bobobeach.com
Sat Apr 9 17:26:57 CEST 2005

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.



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 at 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
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