[BioC] Convert (altcdfenvs)CdfEnvAffy object to useable cdf
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
## I checked that my alt CDF defined the correct subset size of the original
Instance of class CdfEnvAffy:
name : ath1121501cdf
size : 712 x 712
22787 probe set(s) defined.
## I Looked at the intensity values for a specific probeset/gene(all 30 chips).
## 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?
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
More information about the Bioconductor