[BioC] Exon array annotation with limma?

rcaloger raffaele.calogero at gmail.com
Mon Dec 28 15:56:04 CET 2009

 >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.

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


Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
Az. Ospedaliero-Universitaria S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
www:   http://www.bioinformatica.unito.it
Info: http://publicationslist.org/raffaele.calogero

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