[BioC] installing affy environment
Juerg.Straubhaar at umassmed.edu
Mon Sep 8 23:47:35 MEST 2003
The error persists even after loading library(affydata).
From: Tan, MinHan
To: Straubhaar, Juerg
Sent: 9/7/03 10:39 PM
Subject: RE: [BioC] installing affy environment
Don't know if this would work, but try library(affydata) before you run
I had the same problem, which resolved with this command.
From: Straubhaar, Juerg [mailto:Juerg.Straubhaar at umassmed.edu]
Sent: Sunday, September 07, 2003 10:35 PM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] installing affy environment
I created an AffyBatch object with
data <- ReadAffy()
and tried the RMA analysis with
eset <- rma(data)
as described in the Vignette. But this last command gives me the
following comments and error:
Environment mgu74av2cdf is not available.
This environment contains needed probe location information.
We will try to download and install the mgu74av2cdf package.
Note: No specified download type, defaulting to Source
 "Attempting to download mgu74av2cdf from BIOCcdf/"
Error in download.file(fileURL, destFile, mode = "wb", quiet = TRUE,
method = me
unsupported URL scheme
I then tried to download and install the mgu74av2cdf environment
z <- getReposEntry("http://www.bioconductor.org/data/dataRepos")
install.packages2(pkgs="mgu74av2", repEntry=z, searchOptions=F)
This worked, but the original error persisted when trying to use the
'.Library' returns "/usr/lib/R/library" and that is where
install.packages2() installs mgu74av2. I noticed on another machine
where the rma() command worked that the mgu74av2 package
was installed under the affy directory in the R library. I tried the
install.packages2(pkgs="mgu74av2", repEntry=z, searchOptions=F,
This attempt didn't succeed either.
I am grateful for any hint as to how I can successfully perform eset <-
Thank you very much,
University of Massachusetts Medical School
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