[BioC] Error message with ReadAffy

Laurent Gautier laurent at cbs.dtu.dk
Sat Oct 18 08:17:45 MEST 2003

Dear Abhijit Dasgupta,

This is a good point. Having the 'affy' package to load 'affydata'
would solve this problem (at no memory cost since the environments
in the pack affydata only loaded when needed)...
In the released package, this is a bug (the options of the package
should have included 'affydata' in the list of places to look for
cdfenvs). In the 'devel' package,
the dependency to 'affydata' was removed (although I am not sure
of what motivated this change). 



On Fri, Oct 17, 2003 at 06:48:48PM -0400, Dasgupta, Abhijit (NIH/NCI) wrote:
>  Why doesn't affy, if it encounters a cel file from a HG-U133A chip, search
> first in the affydata library (or try to download it)for the CDF file
> instead of giving the error message Xuejun got (and I got earlier). I guess
> my question is, why do we have to manually load the affydata library? This
> is a point I didn't find in any of the affy vignettes, though if I missed it
> I'm sorry.
> Abhijit Dasgupta
> Division of Cancer Epidemiology and Genetics
> National Cancer Institute
> -----Original Message-----
> From: Xuejun Peng
> To: bioconductor at stat.math.ethz.ch
> Sent: 10/17/2003 3:00 PM
> Subject: [BioC] Error message with ReadAffy
> I'm running Bioconductor release 1.2 with R 1.7.1 in a Windows 2000 
> environment. I encoutered the following problem when I try to read affy 
> data. Can anyone help?
> (I did not have this problem with older versions.)
> Thanks.
> Peng
> *************************************************
>  ReadAffy("NAWM17_10_4A.cel")
> Environment hgu133acdf is not available.
> This environment contains needed probe location information.
> We will try to download and install the hgu133acdf package.
> Note: No specified download type, defaulting to Win32
> [1] "Attempting to download hgu133acdf from BIOCcdf/"
> Error in download.file(fileURL, destFile, mode = "wb", quiet = TRUE, 
> method = method) :
>         unsupported URL scheme
> Error in inherits(cdf.env, "try-error") : Object "cdf.env" not found
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Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent

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