[BioC] cdf for ATH1 array

[James W. MacDonald]

William Robert Swindell wrote:
> Dear Bioconductor,
> I have been trying to generate gcrma expression estimates from CEL files, 
> and I obtain the error message shown below. The CEL files were generated 
> from the Arabidopsis ATH1 array. The error message suggests that 
> bioconductor does not have the cdf file for the ATH1 array....is that 
> correct?
> Thanks very much,
> William R. Swindell
> Michigan State University 
> 
> 
>>library(affy)
>>mydata = ReadAffy()
>>library(gcrma)
>>eset = gcrma(mydata) 
>>
> 
> 
> Computing affinities[1] "Checking to see if your internet connection 
> works..."
> Warning message:
> cannot open: HTTP status was '404 Not Found'
> Note: http://www.bioconductor.org/CRANrepository does not seem to have a 
> valid repository, skipping
> Warning message:
> Failed to read replisting at http://www.bioconductor.org/CRANrepository in: 
> getReplisting(repURL, repFile, method = method)
> Warning message:

This doesn't imply that the package is not there - HTTP status was '404 
Not Found' means that you couldn't connect to the BioC webserver. Likely 
possibilities are
a.)BioC was down when you tried (it's up now), or
b.) MSU uses a proxy server and you need to set your R to use the 
internet2.dll (assuming you are on Windows - you don't mention your OS). 
If this is true, see FAQ 2.19

http://cran.fhcrc.org/bin/windows/base/rw-FAQ.html#The-Internet-download-functions-fail_002e

HTH,

Jim


> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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