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

> 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) What happens if you do: library(mgu74av2) ?

Hi Jeff, There is no change, the error persists: library(mgu74av2) eset <- rma(data) ... Error in download.file(fileURL, destFile, mode = "wb", quiet = TRUE, method = method) : unsupported URL scheme -----Original Message----- From: Jeff Gentry To: Straubhaar, Juerg Cc: bioconductor@stat.math.ethz.ch Sent: 9/8/03 10:38 AM Subject: Re: [BioC] installing affy environment > 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) What happens if you do: library(mgu74av2) ?

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@umassmed.edu] Sent: Sunday, September 07, 2003 10:35 PM To: bioconductor@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 _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor 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.