[BioC] How to create a custom CDF ?

Alexander Stoddard astoddar at mail.med.upenn.edu
Wed Jun 30 20:55:31 CEST 2004

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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