[BioC] Importing CDF file for custom array using makecdfenv

[Ann Hess]

I have CEL (and CDF) files from a custom Affy chip and I need to import 
the CDF file into BioConductor.  I am using R 2.3.1, Bioconductor 1.8 and 
Windows XP.

I have read the makecdfenv vignette and other postings about this process, 
but I can't figure out how to make it work!  I have the original CDF file 
in the same directory as my CEL files.  I have downloaded ActivePerl 
and the R source package installation files as suggested in the makecdfenv 
vignette (although I don't understand how these are used).

After loading affy and reading in the CEL files (into an affybatch object 
called "data"), I used the following 
commands:
library(makecdfenv)
make.cdf.package("XXX.cdf",species="XXX")
XXXcdf=make.cdf.env("XXX.cdf")

I do not get any errors, but when I try to look at the affybatch object I 
get the following message:

Error in getCdfInfo(object) : Could not obtain CDF environment, problems 
encountered:
Specified environment does not contain XXX
Library - package XXXcdf not installed
Data for package affy did not contain XXXcdf
Bioconductor - XXXcdf not available
AffyBatch object
size of arrays=291x291 features (15887 kb)
cdf=XXX (??? affyids)
number of samples=24
Error in getCdfInfo(object) : Could not obtain CDF environment, problems 
encountered:
Specified environment does not contain XXX

I have tried putting the CDF file (created by BioC) in the R libraries 
folder with other libraries, but no luck.

In the makecdfenv vignette it says to "open a terminal with an operating 
system shell and write R CMD INSTALL XXXcdf", but I don't know how to do 
this on windows.

Any suggestions would be greatly appreciated!

Ann