[BioC] affy hugene 2.1 st

[James W. MacDonald]

Hi Dario,

On 8/20/2012 1:36 AM, Dario Greco wrote:
> dear friends,
> we are starting a project using the new affymetrix human gene 2.1 st chips.
> i would like to know:
> 1) does anyone have yet any experience with them? any opinion/particular note analysing them?
> 2) what is the bioc roadmap for including the cdf/annotation packages for this?

There won't be a cdf package created by us. Instead there will be a 
pd.hugene.2.0.st.v1 package, intended for use with the oligo package. 
Note that there hasn't been an unsupported cdf file for any Gene ST 
chips after version 1.0, although Philip de Groot has been making cdf 
packages for the 1.1 chips, and may well make them for the 2.0 and 2.1.

http://nmg-r.bioinformatics.nl/NuGO_R.html

As for a roadmap, these packages will be part of the new BioC release.


> 3) what is the roadmap for the alternative cdf packages?

We don't make those; Manhong Dai at MBNI does. I suggest you ask him. 
You can get his email off their website:

http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp

Best,

Jim


>
> thanks you so much for your kind reply.
> cheers
> dario
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099