Question: zebrafish annotation
0
gravatar for Bio Sam
11.1 years ago by
Bio Sam60
Bio Sam60 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
annotation zebrafish • 465 views
ADD COMMENTlink modified 11.1 years ago by Marc Carlson7.2k • written 11.1 years ago by Bio Sam60
Answer: zebrafish annotation
0
gravatar for Marc Carlson
11.1 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
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: http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html Please let me know if you have any questions, Marc 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 >
ADD COMMENTlink written 11.1 years ago by Marc Carlson7.2k
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