[BioC] installing affy environment

Straubhaar, Juerg 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 
[1] "Attempting to download mgu74av2cdf from BIOCcdf/"
Error in download.file(fileURL, destFile, mode = "wb", quiet = TRUE, method = me
thod) : 
	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,

Juerg Straubhaar
University of Massachusetts Medical School

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