[BioC] Cannot open compressed file

[Robert Gentleman]

On Wed, Nov 19, 2003 at 03:11:46PM -0500, Simon, Richard (NIH/NCI) wrote:
> I'm running R 1.8 on a Windows XP professional box.
> I tried to import a few  U133 .cel files and run rma after downloading all
> of the bioconductor packages.
> 
> repdata <- ReadAffy()
> eset <- rma(repdata)
> 
> I first got a message that it autodownloaded  hgu133atagcdf and that
> installation was complete.
> 
> Then I got an error in open.connection (con,"rb") unable to open connection
> 
> Then I got a 
> 
> warning cannot open compressed file
> 'C:/PROGRA~1/R/rw1080/library/hgu133atagcdf/data/hgu133atagcdf.rda
> 
> Then
> 
> error in library("hgu133atagcdf",lib.loc="C:PROGRA~1/R/rw1080/library")
> .First.lib failed 
> 
> This is my first attempt to use bioconductor. I didn't get very far. Can
> anyone suggest what is wrong?

 Hi,
  a little disagreement about who is supposed to unzip what, we should
  be able to fix this up on our end shortly. A "quick fix" on your end
  is to find the directory that the library is installed in 

  C:/PROGRA~1/R/rw1080/library/hgu133atagcdf/data/

 and in that directory you will find a file named Rdata.zip, if you
 unzip it, then all should be well (or at least you get past this
 error, I have no 133atag CEL files to see what one might need to do
 differently from that point on.

 Thanks for pointing this out (with enough detail to fix it),

   Robert

> 
> Thanks,
> 
> Rich Simon
> 
> Richard Simon, D.Sc.
> Chief, Biometric Research Branch
> Head, Computational & Systems Biology Group
> Division of Cancer Treatment & Diagnostics
> National Cancer Institute
> 
> 
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> 
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| Robert Gentleman                 phone : (617) 632-5250                   |
| Associate Professor              fax:   (617)  632-2444                   |
| Department of Biostatistics      office: M1B20                            |
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