[BioC] agilent zebrafish array annotation

Georg Otto georg.otto at tuebingen.mpg.de
Thu Apr 17 14:47:50 CEST 2008


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.



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