Hi Ben, this is something I have done a lot and basically this is what you
need to do

if you are running windows, these instructions will help you set up your
system to build/install R packages
Read the instructions in the help file R Installation and Administrations
for The Windows toolset.
go to www.murdoch-sutherland.com/Rtools and follow the instructions

# assuming your probes.txt is the same format as the probes tab files from
affy
library(makecdfenv)
make.cdf.package("XYZ.cdf",species="Homo_sapiens",cdf.path="C:/Data/CDFs/")
makeProbePackage("XYZ",
                 datafile   = gzfile("XYZ_probes.txt", open="r"),
                 outdir     = ".",
                 maintainer = "me <me@mine.com>",
                 version    = "0.0.1",
                 species    = "Homo_sapiens",
                 check      = FALSE,
                 force      = TRUE)

# install the probe and cdf packages
# open a dos prompt
R CMD INSTALL XYZcdf
R CMD INSTALL XYZprobe

## or alternatively select do the following to build the packages
R CMD BUILD --binary --auto-zip XYZcdf
R CMD BUILD --binary --auto-zip XYZprobe


hope this helps

claire

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