[BioC] Exon array annotation with limma?

[rcaloger]

Martin Morgan ha scritto:
> 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
>   
Hi Martin,
sorry about it, I missed that message!

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


-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
Az. Ospedaliero-Universitaria S. Luigi
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email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
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