Hi,
I have the original cdf file from Affymetrix web page
(Cytogenetics_Array.CDF)  in my working directory and I tried the
following... Lenka

> library(makecdfenv)

>  make.cdf.package("Cytogenetics_Array.cdf", cdf.path = getwd(), compress =
FALSE, species = "Homo_sapiens")
Error in make.cdf.env(filename, cdf.path = cdf.path, compress = compress,  :

  makecdfenv does not currently know how to handle cdf files of this type
(genotyping).

> sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32
locale:
[1] LC_COLLATE=Czech_Czech Republic.1250  LC_CTYPE=Czech_Czech
Republic.1250
[3] LC_MONETARY=Czech_Czech Republic.1250
LC_NUMERIC=C
[5] LC_TIME=Czech_Czech Republic.1250
attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
[8] base
other attached packages:
[1] makecdfenv_1.24.0 affyio_1.14.0     affy_1.24.2       Biobase_2.6.1
loaded via a namespace (and not attached):
[1] preprocessCore_1.8.0

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