[BioC] zebrafish annotation

Marc Carlson mcarlson at fhcrc.org
Tue Sep 16 20:09:36 CEST 2008

Hi Sam,

We aren't going to leave you behind.

In fact, zebrafish support has already been added to the devel branch of 
bioconductor and will be pushed to the upcoming release branch very 
soon.  Additionally, I am probably a day away from pushing a second 
version of zebrafish support online into the devel branch and this 
second push will contain support for ZFIN IDs and so I strongly 
recommend that you wait for that.  The package formerly called 
"zebrafish" is also going to become zebrafish.db with this next push 
which should help modernize things for you if you are using that 
platform.  In any case if you still need to make chip packages for 
zebrafish all you should have to do is use the appropriate SQLForge 
functions in AnnotationDbi.  You can find a vignette on the subject here:


Please let me know if you have any questions,


Sam Hunter wrote:
> Hi Marc, and the Bioconductor mailing list,
> I do a fair amount of work with the Affymetrix Zebrafish platform, but
> the recent move to .db annotation files seems to have left zebrafish
> behind.  From what I've read in previous posts to the Bioconductor
> list, the new .db annotation packages are not easy to generate for the
> end-user, but might be made available upon request.  Is this still the
> case?
> If so, is there any possibility of generating this annotation file so
> that all of the packages which rely on "zebrafish_dbconn" will work
> properly once again?
> thanks,
> Sam

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