[BioC] Exon array annotation with limma?

[rcaloger]

Hi,
I am the maintainer of oneChannelGUI,
concerning gene-level annotation for exon array, oneChannelGUI uses an internal annotation, builded parsing the netaffx annotation data via AffyCompatible package. The function buildingLocalAnnotation() produces a R object containing a data frame with the following columns for gene-level data:
PROBESETID       ACC   SYMBOL             DESCRIPTION CYTOBAND
The internal annotation is updated when a new release of netaffx annotation is avilable. Users can build the annotation themselves with the previously described function. 
Cheers
Raffaele
P.S. oneChannleGUI also provides an internal annotation for exon-level probesets.
This internal annotation will be replaced by three annotation packages, now present in the devel branch:
http://www.bioconductor.org/packages/2.6/data/annotation/html/HuExExonProbesetLocation.html
http://www.bioconductor.org/packages/2.6/data/annotation/html/MoExExonProbesetLocation.html
http://www.bioconductor.org/packages/2.6/data/annotation/html/RaExExonProbesetLocation.html



>Hello James,

>"Error in .checkKeys(value, Lkeys(x), x at ifnotfound) :
   value for "3948543_at" not found"

>You're right, it's a mismatch problem; I just looked at all the "_at" 
>probes in the db file and their id is not even right - some are 9994_at, 
>which have no equivalent for the transcript clusters ids on my chip, 
>which are of the format "3948543" - always 7 digits.

>I don't know why is it so in the db file, but it doesn't match anything 
>on my chip, nor on NetAffx, so I don't know why the MBNI folks did it 
>like so.

>My next options are to look at the source code of onechannelGUI (which 
>doesn't use the MBNI file to accomplish its magic) or try to fix my 
>RCurl / Biomart problem. I'll probably open a new mailing list topic for 
>this one. Much frustration so far with the exon array chip workflow, 
>it's so unlike the other chips; there really should be a wiki for this  :) 

>Thanks for the help,
>Michael


----------------------------------------
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
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Mobile ++39 3333827080
email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
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