[BioC] How to create a custom CDF ?

Ben Bolstad bolstad at stat.berkeley.edu
Wed Jun 30 21:00:41 CEST 2004

There is such a CDF package for  mgu74a and mgu74av2  at



On Wed, 2004-06-30 at 11:55, Alexander Stoddard wrote:
> Greetings all,
> I am interested in using the gcrma method to analyze a set of data  that 
> extends over the mgu74av1 and mgu74av2 Affy chips.
> I suppose my best bet is to create a custom CDF environment and Probe 
> package which contain only the common probesets across the two versions. 
> Does this seem reasonable?
> I  can think of two ways to approach this: 
> 1) create custom files representing the Affy CDF and probe files (this I 
> believe I can do). Then use tools in Bioconductor to create the R 
> packages. I guess those include makecdfenv (with which I am not 
> familiar) and whatever is needed to create the probe data.
> 2)  work with R to extract the common data from the existing packages 
> into new ones.
> I would welcome advice on which would be easier plus some pointers on 
> what I need to do in R to achieve either one.
> If I am successful would such a combined mgu74av1 and mgu74av2 CDF 
> environment  be  of  sufficient  interest  to  others  to make  
> generally available?
> Many thanks,
> Alex Stoddard
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Ben Bolstad <bolstad at stat.berkeley.edu>

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