[BioC] How to create a custom CDF ?
astoddar at mail.med.upenn.edu
Wed Jun 30 20:55:31 CEST 2004
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
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