[BioC] makecdfenv windows XP

James W. MacDonald jmacdon at med.umich.edu
Wed Dec 15 17:55:19 CET 2004

Malick Paye wrote:
> Hello all,
> I have a custom chip and I'm following the directions at: 
> http://www.bioconductor.org/repository/devel/vignette/makecdfenv.pdf 
> to try to make a CDF for my custom chip, and running into some troubles. 
> When i try to run  make.cdf.env i have the following message : 
> " Reading CDF file.
> Error in getInfoInFile(file, "CDF", unit = "Chip", property = "Name",  : 
>         Cannot open the file C:/Program Files/R/rw2001/myfile.cdf."

Is the cdf file really in your R_home directory, or is it somewhere 
else? If so, you need to either change your working directory to the 
location of the cdf file, or you need to explicitly state the location 
in your call to make.cdf.env().

One other possibility (if the cdf is where R is looking), is that the 
cdf is in binary format. You can test this by opening the cdf using 
WordPad. If you can't read anything, it is binary.

Affy is changing from text to binary format for the cdf files, and we 
don't yet have the functions to handle the binary format. Binary 
compatibility is being worked on, and should be done soon.


> I would probably need some additional tools to get it working, but i don't know wich one to install. 
> Thanks,
> Malick,
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James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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