[BioC] installing affy environment
Juerg.Straubhaar at umassmed.edu
Sun Sep 7 23:35:03 MEST 2003
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 manually with
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 rma() function.
'.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 command
install.packages2(pkgs="mgu74av2", repEntry=z, searchOptions=F, lib="/usr/lib/R/library/affy/data")
This attempt didn't succeed either.
I am grateful for any hint as to how I can successfully perform eset <- rma(data).
Thank you very much,
University of Massachusetts Medical School
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