[BioC] installing affy environment

Straubhaar, Juerg Juerg.Straubhaar at umassmed.edu
Mon Sep 8 23:47:35 MEST 2003

Hi Min-Han,

The error persists even after loading library(affydata).

Thank you,

-----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

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


-----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


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

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,

Juerg Straubhaar
University of Massachusetts Medical School

Bioconductor mailing list
Bioconductor at stat.math.ethz.ch
This email message, including any attachments, is for the sole use of
the intended recipient(s) and may contain confidential information.  Any
unauthorized review, use, disclosure or distribution is prohibited.  If
you are not the intended recipient(s) please contact the sender by reply
email and destroy all copies of the original message.  Thank you.

More information about the Bioconductor mailing list