[BioC] Annotation in Agi4x44PreProcess

[Marc Carlson]

Hi Samantha,

Have you considered just generating an annotation package using the
SQLForge code in AnnotationDbi?  There is a SQLForge vignette explaining
how to do this here as well as other explanations on how to use the
annotation packages:

http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.html

For those ensembl transcript IDs, you could convert them to entrez gene
annotations 1st using the org.Dr.egENSEMBLTRANS mapping in the
org.Dr.eg.db package and then simply follow the example in the vignette
above.  Let us know if you have questions about how to do this stuff
after looking over the AnnotationDbi vignettes.


  Marc



On 07/16/2010 08:20 AM, Samantha England wrote:
> The raw text files generated by the Agilent Feature Extraction software contain the probe and gene name for each spot on the array.  We also have a custom designed gal file.  The problem we have is that only 5 zebrafish-specific annotation databases exist for zebrafish: four of these have been designed for use with the Affymetrix zebrafish chip, whilst the remaining database uses entrez ids.  Our gene names are predominantly listed as ENSEMBL transcript identifiers (only a small proportion are entrez ids).  Therefore there doesn't yet exist an appropriate annotation database for use with our data.  With this in mind I have two questions: