[BioC] help for canine 2.0 arrays

James W. MacDonald jmacdon at med.umich.edu
Fri Sep 14 19:32:30 CEST 2007


Hi Wei,

You seem to be having problems connecting to the repository. Does

source("http://www.bioconductor.org/biocLite.R")
biocLite("canine2cdf")

work for you?

You should also always give your sessionInfo(). It may be that you have 
a very old R version for which there isn't a canine2cdf (in which case 
you should upgrade to R-2.5.1 at the very least).

Best,

Jim

Wei Wang wrote:
> Hi, all,
> 
> I'm at Cornell university. I'm trying to use the affy package to analyze
> canine 2.0 arrays, I can read in CEL files into "myAffyBatch", but running
> show(myAffyBatch) give error below, could someone help (human arrays work
> fine for me)? Thanks a lot.
> 
> Wei
> 
> "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:
> cannot open: HTTP status was `403 Forbidden'
> Note: http://www.bioconductor.org/repository/devel/package/Source does not
> seem to have a valid repository, skipping
> Warning messages:
> 1: Failed to read replisting at
> http://www.bioconductor.org/repository/devel/package/Source in:
> getReplisting(repURL, repFile, method = method)
> 2: cannot open: HTTP status was `403 Forbidden'
> Note: http://www.bioconductor.org/repository/devel/package/Win32 does not
> seem to have a valid repository, skipping
> Note: You did not specify a download type.  Using a default value of: Win32
> This will be fine for almost all users
> 
> Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> encountered:
> Specified environment specified did not contain Canine_2
> Library - package canine2cdf not installed
> Data for package affy did not contain Canine_2
> Bioconductor - canine2cdf not available
> In addition: Warning message:
> Failed to read replisting at
> http://www.bioconductor.org/repository/devel/package/Win32 in:
> getReplisting(repURL, repFile, method = method)
> "
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623



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