[BioC] Mapping50K cdf environment

[James W. MacDonald]

Tim Strom wrote:
> I tried to generate a cdf packages with
> make.cdf.package
> for the Mapping50K chips.
> I got the error message that cdf packages
> can not be generated for this type of
> chips.
> 
> Is there any other way to generate
> the cdf packages?

Yes. The makePlatformDesign package in the devel repository has 
functionality to make these packages. You will need the cdf, the FASTA 
probe sequences, and the csv annotation file (all available on Affy's 
website). This package is still quite developmental - the only 
information about the functions is the comments in the code. In 
addition, there is only a source version available, so if you are on 
windows or MacOS, you will have to get set up to build source packages.

In addition, these mapping cdfs are quite large. On a 64 bit OS with 16 
Gb RAM, it only takes about 15 minutes to build the package. On my 
pitiful win32 box with 2 Gb of RAM I start swapping almost 
instantaneously, so I have to let it run overnight.

The makePlatformDesign package is the next generation version of 
makecdfenv, and is designed to work with the oligo package (the next 
generation version of affy). Unfortunately, I have not had the time this 
Summer to add the basic accessor functions to oligo for the SNP chips, 
not to mention any higher level functionality, so simply building the 
PDenv for a given chip will not allow you to do any analyses without 
some further code writing.

If you are looking for analysis tools that already exist, Affy's GDAS 
and copy number tool are one route, and I believe dChipSNP will now work 
with the 100K chips as well (I see a paper in last week's Nature where 
they use dChipSNP on 100K chips).

HTH,

Jim


> 
> Thanks
> Tim
> 
> 
> --------------------------------------------------------------
> 
> Tim M. Strom				Tel: +49 89 3187 3296
> Institut fuer Humangenetik		Fax: +49 89 3187 3297
> Ingolstaedter Landstr. 1
> 85764 Neuherberg
> Germany
> 
> WWW: http://ihg.gsf.de
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623