[BioC] Exon array annotation with limma?

[Martin Morgan]

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.

Developers are reminded that it is NOT appropriate for new features to
be added to the release branch of Bioconductor. More detail is provided here

  https://stat.ethz.ch/pipermail/bioc-devel/2009-December/002079.html

Best,

Martin

> Cheers
> Raffaele
> P.S: let me know if these functions fulfill your needs, I will be happy
> to improve them upon suggestion
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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