[BioC] agilent zebrafish array annotation

[Marc Carlson]

Georg Otto wrote:
> Hi,
>
> I started to use the agilent zebrafish array and I am using
> bioconductor packages (limma and others) for the data analysis as I
> did already with the Affymetrix zebrafish array. I noticed that unlike
> for the Affymetrix zebrafish array, there is no annotation package for
> the Agilent zebrafish array, but there are packages for the Agilent
> human, mouse and rat arrays.
>
> Since I have some experience in creating custom annotation
> environments (e.g. using biomart) I would be willing to volunteer in
> generating an annotation package for the Agilent zebrafish
> array. However, it is not quite clear to me, how for example the
> mgug4104a.gb or other packages of this kind were generated. Reading
> the vignettes of the AnnBuilder and AnnotationDbi packages did not
> help me very much either.
>
> Therefor my question is: Is the package creation process documented
> somewhere? Is the code for the package generation available somewhere?
> As I said, I would be willing to generate the annotation package and
> contribute this to the community, but I do not know where to start.
>
> Best,
>
> Georg
>
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>   

HiGeorg,

Right now there are two styles of annotation package.  The newer format 
is generated from code in the very latest bleeding edged version of 
AnnotationDbi (from the devel branch), and the older format is generated 
from AnnBuilder.  It is preferable to use the newer code in 
AnnotationDbi, but this requires that your organism be supported first.  
As of right now, zebrafish is not a supported organism for the newer 
packages, but this is not set in stone.  If you would be willing to work 
with me a little bit and be slightly more patient, we can try to rectify 
this situation together, but otherwise you are going to have to use the 
older AnnBuilder package to make your zebrafish packages. 

Making a vignette for AnnBuilder is mostly about calling the 
ABPkgBuilder() function with the correct parameters and using properly 
formatted inputs.  Once zebrafish is a supported organism, the process 
for making a new package using AnnotationDbi's SQLForge functions would 
be very similar.  I will be happy to help you with either of these 
processes.


    Marc