[BioC] Exon array annotation with limma?

Michael Imbeault michael.imbeault at sympatico.ca
Mon Jan 4 21:23:15 CET 2010

Hello Raffaele,

Thanks a lot, works beautifully, adding much needed functionality to 

Happy New Year,

On 28/12/2009 9:56 AM, rcaloger wrote:
> >Michael wrote:
> >Hello Raffaele,
> >Interesting; do you think you could provide a package to provide the 
> same functionality that is present in oneChannelGUI (for gene-level 
> annotation, that is)? I looked >at the code and it's a bit interwined 
> with the onChannelGUI environment; is there an easy way to extract the 
> data frame and save it as one external to the environment >in the 
> mean-time?
> >I can see from some mailing list topics that an easy to use 
> gene-level annotation solution for exon arrays is really needed.
> >
> >Thanks,
>> Michael
> Dear Michael,
> I have created two stand-alone functions for gene level annotation for 
> exon-arrays, which are available as part of oneChannelGUI package but 
> can be used without the oneChannelGUI interface.
> The function standAloneBuildingLocalAnnotation creates a data frame 
> with gene-level annotation data for exon arrays (human, mouse or rat) 
> using the netaffx database informations.
> The function standAloneAddingAnnotation attaches gene-level annotation 
> to a data frame.
> You will find more info on the functionalities of these functions in 
> the vignette associated to oneChannelGUI release 1.12.4. I uploaded 
> the package on 28th December and I am expecting that it will be 
> available on the Bioconductor web in 24 hours.
> Cheers
> Raffaele
> P.S: let me know if these functions fulfill your needs, I will be 
> happy to improve them upon suggestion

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