[BioC] annotation and GO for non-model organism

[Wolfgang Huber]

Hi Ingunn

you could check out the Category package, which has tools for detecting 
association between gene annotation categories and differential 
expression contrasts - see its vignette.

Best wishes
      Wolfgang

-------------------------------------------------------
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
-------------------------------------------------------

  Berget wrote:
> 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
> 
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