[BioC] annotation for new agilent arrays

Fri Aug 27 10:50:38 CEST 2010

Dear Marc and Francois,

I have just gone through the process of retrieving the new annotation
files from Agilent's earray web site and I can confirm that is *is* a 
pain. :-)

Of course I'll be more than happy to make a contribution in exchange for
the first-class software and support we have enjoyed for many years and
I'm probably better in dealing with annotation than in devising innovative
statistical methods anyway... so I'll have a look at the 
packages/vignettes 
Marc has mentioned and will for sure come back with further questions...

Cheers,

 - axel

Axel Klenk
Research Informatician
Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 
Switzerland

From:
Marc Carlson <mcarlson at fhcrc.org>
To:
Francois Pepin <francois at sus.mcgill.ca>
Cc:
bioconductor at stat.math.ethz.ch
Date:
26.08.2010 18:45
Subject:
Re: [BioC] annotation for new agilent arrays
Sent by:
bioconductor-bounces at stat.math.ethz.ch

Hi Francois,

The troublesome part is not really adding things into the pipeline for
building, it's the fact that Agilent does not make it easy for me to
automate updates for their probe mapping files.  When you combine that
with the fact that we are already building, checking and hosting about
120 annotation packages twice a year here you can hopefully see that
this process is not truly devoid of cost.  The result is that it's never
quite as simple as just pushing a button to get all these things built,
checked, and tested etc.  Most of it is automatic, but some of it (like
getting new mapping files from Agilent (or other more boutique
platforms) cannot be easily automated.  Having package contributors is
also not free of cost.  I do still have to bother them twice a year and
make sure that things get built correctly etc.  But it is still a big
win for the project to have people contribute because it means that we
cover more ground from more different kinds of platforms than I might
think to include on my own and also because it means that we can support
more packages overall right out of the box.

So I guess what I am saying is that package contributors are extremely
helpful to the project and should always be encouraged.  ;)

If you have some ideas for how I can make this even more automatic and
want to discuss it further I would be happy to, but at this point we
should probably consider taking it offline as I think the discussion is
maybe no longer relevant to the entire thread.  ;)

  Marc

On 08/25/2010 04:52 PM, Francois Pepin wrote:
> Hi Marc,
>
> How much work would it be to just include those in your pipeline?
>
> The process should be exactly the same as for the current agilent arrays 
(like hgug4112a, mgug4122a). Considering the current use of Agilent 
arrays, I think the new versions are going to be relatively widely used 
for a bit longer.
>
> Francois
>
> On Aug 25, 2010, at 1:58 PM, Marc Carlson wrote:
>
> 
>> Hi Axel,
>>
>> We always welcome new annotation packages.  But be warned that you 
would
>> be expected to maintain them and provide a updated version of them for
>> each release of Bioconductor.  That works out to me sending you an 
email
>> (requesting an update) twice a year.  The SQLForge package should allow
>> you to make a new annotation package.  You can see the vignette that is
>> bundled in the AnnotationDbi package for details.
>>
>>
>>  Marc
>>
>>
>>
>> On 08/25/2010 08:37 AM, axel.klenk at actelion.com wrote:
>> 
>>> Dear Bioc list and esp. Marc, 
>>>
>>> are there any plans to include annotation for the new Agilent 4x44K 
v2/v3
>>> and 8x60K arrays in one of the next releases of Bioconductor? As far 
as I
>>> understand the non-control oligo set is the same for 4x44K v2 and 
8x60K.
>>> We'd be interested in human (G4845A), mouse (G4868A) and rat (G4847B)
>>> in particular.
>>>
>>> If not, and if I should succeed in creating such packages myself :-), 
>>> would 
>>> you want to obtain and distribute the results of these efforts?
>>>
>>> Cheers,
>>>
>>> - axel
>>>
>>>
>>> Axel Klenk
>>> Research Informatician
>>> Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / 

>>> Switzerland
>>>
>>>
>>>
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