[BioC] annotation and GO for non-model organism

[Ingunn Berget]

Dear List

I want to do GO analysis on my microarray results, and have not done this before. We have a cDNA array for a non-model organism. The manufacturers of the array have provided annotations, so I have
Accesision number, gene description, gene synonyms, EC, molecular_function, biological_process, cellular_component, InterPro, KEGG, Pfam, EMBL, Ensembl, UniGene, RefSeq, PROSITE, GeneId, org, 
and more in a tab delimited txt file.

so I suppose I have all the information I need, how can I use this with the bioconductor packages?

I have looked at the vignette for SQLForge in the AnnotationDbi package as suggested on this list before, but as it says "At the present time, it is possible to make annotation packages for the
most common model organisms" I don't know how to proceed.

Best regards
Ingunn