[BioC] Exon array annotation with limma?
michael.imbeault at sympatico.ca
Mon Jan 4 21:23:15 CET 2010
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
> >I can see from some mailing list topics that an easy to use
> gene-level annotation solution for exon arrays is really needed.
> 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.
> P.S: let me know if these functions fulfill your needs, I will be
> happy to improve them upon suggestion
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