Dear Michael,

Since we are entering in the winter holiday and I have some spare time, I
will create a stand-alone function for gene level annotation for exon-arrays
using as input a data frame, that can be generated by limma or other
statistical tools.

On Wed, Dec 23, 2009 at 6:42 AM, Michael Imbeault <
michael.imbeault@sympatico.ca> 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?
>
In the mean time you can extract the anntoationd ata frame using:
data("huex.annotation",package="oneChannelGUI") #for human
data("moex.annotation",package="oneChannelGUI")#for mouse
data("raex.annotation",package="oneChannelGUI")#for rat

In the release of oneChannelGUI 1.12.2 (22 December 2009) of stable
Bioconductor 2.5 you can find the latest annotations released from
Affymetrix in november
Cheers
Raffaele

>
> 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@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@unito.it
>>      raffaele[dot]calogero[at]gmail[dot]com
>> www:   http://www.bioinformatica.unito.it
>> Info: http://publicationslist.org/raffaele.calogero
>>
>>
>>
>>


-- 
----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero@unito.it
         raffaele[dot]calogero[at]gmail[dot]com
www:   www.bioinformatica.unito.it

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