[BioC] Convert (altcdfenvs)CdfEnvAffy object to useable cdf package

Rhonda DeCook rdecook at iastate.edu
Wed Mar 9 19:02:40 CET 2005


I successfully created a new CDF environment for the ATH1 chip awhile ago using 
the altcdfenv package.  I'll show you some of the code that worked for me...  

## I built my new cdf environment (using a function similar to 
> alt.cdf.all<-buildCdfEnv.pmids(pm.i.all.new.2, altcdfname="alt.cdf.ath1", 

## I reassigned the CDF environment of my old affybatch:
> cel.files.30.lines at cdfName<-alt.cdf.all at envName
> cdfName(cel.files.30.lines)                
[1] "alt.cdf.ath1"

## I checked that my alt CDF defined the correct subset size of the original 
22810 probes:
> alt.cdf.object<-wrapCdfEnvAffy(alt.cdf.ath1,712,712,"ath1121501cdf")
> print(alt.cdf.object)
Instance of class CdfEnvAffy:
 name     : ath1121501cdf 
 chip-type: ath1121501cdf 
 size     : 712 x 712 
 22787 probe set(s) defined.

## I Looked at the intensity values for a specific probeset/gene(all 30 chips).
> pm(cel.files.30.lines,gene="262199_at")

## Other functions applied to the affybatch used only my subsetted list of 
genes defined by the alternative cdf, as I wanted.


> I apologize for re-posting..I'd originally posted this as "Can't normalize 
> with alternative affy CDF environment."
> After some more searching, I think the problem is that once I have a 
> CdfEnvAffy class object which was made according to the altcdfenvs tutorial, 
> how do I take that object and convert it into either a CDF package or a CDF 
> environment that can actually be used with an affybatch object?
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