[BioC] installing affy environment

[Straubhaar, Juerg]

Hi Min-Han,

The error persists even after loading library(affydata).

Thank you,
Juerg

-----Original Message-----
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
rma.

I had the same problem, which resolved with this command.

Min-Han

-----Original Message-----
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


Hi,

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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