[BioC] Exon array annotation with limma?

Michael Imbeault michael.imbeault at sympatico.ca
Wed Dec 23 06:42:54 CET 2009


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

On 22/12/2009 9:12 AM, rcaloger wrote:
> 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
> Lab.   ++39 0116705408
> Fax    ++39 0119038639
> Mobile ++39 3333827080
> email: raffaele.calogero at unito.it
>       raffaele[dot]calogero[at]gmail[dot]com
> www:   http://www.bioinformatica.unito.it
> Info: http://publicationslist.org/raffaele.calogero
>
>
>



More information about the Bioconductor mailing list