[BioC] making a cdf package for a custom affymetrix array

[James W. MacDonald]

Hi Lauren,

On 11/6/2012 9:11 PM, Lauren Sassoubre wrote:
> Hi,
> This error message has come up in previous posts but I haven't found a solution that works. I'm having trouble loading a cdf file for a custom array and using that cdf for the function ReadAffy. Below are the code and error message. What does this error mean? I have tried reinstalling R and deleting the cdf files and reloading them from the original disk. I'm working with the most recent version of R for Macs.
> Thanks in advance for the help!
> Lauren
>
>> make.cdf.env("Gilmorea520817.cdf")
> Error in isCDFXDA(file.path(path.expand(cdf.path), filename)) :
>    Unable to open the file /Users/lmsassoubre/Desktop/solarsimandmicroarrays/CD_Gilmorea520187F/Full/Gilmorea520817.cdf

There are two obvious possibilities. First, the file might not be in the 
path you specify. For example:

 > dir(".", "nopackage.cdf")
character(0)
 > make.cdf.env("nopackage.cdf")
Error in isCDFXDA(file.path(path.expand(cdf.path), filename)) :
   Unable to open the file /misc/staff/jmacdon/nopackage.cdf

alternatively, you might not have read permissions. This is much less 
likely, especially if you are copying the file and running R as the same 
user. To make the below work, I had to change permissions to a state 
that is unlikely to exist in that situation. However unlikely, it is 
still a possibility:

 > system("ls -lah AG.CDF")
--wx------ 1 jmacdon staff 20M Nov  7 07:13 AG.CDF
 > make.cdf.env("AG.CDF")
Error in isCDFXDA(file.path(path.expand(cdf.path), filename)) :
   Unable to open the file /misc/staff/jmacdon/AG.CDF

I suppose there are other alternatives as well, but none come readily to 
mind.

Best,

Jim


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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099