I'm running R 1.8 on a Windows XP professional box. I tried to import a few U133 .cel files and run rma after downloading all of the bioconductor packages. repdata <- ReadAffy() eset <- rma(repdata) I first got a message that it autodownloaded hgu133atagcdf and that installation was complete. Then I got an error in open.connection (con,"rb") unable to open connection Then I got a warning cannot open compressed file 'C:/PROGRA~1/R/rw1080/library/hgu133atagcdf/data/hgu133atagcdf.rda Then error in library("hgu133atagcdf",lib.loc="C:PROGRA~1/R/rw1080/library") .First.lib failed This is my first attempt to use bioconductor. I didn't get very far. Can anyone suggest what is wrong? Thanks, Rich Simon Richard Simon, D.Sc. Chief, Biometric Research Branch Head, Computational & Systems Biology Group Division of Cancer Treatment & Diagnostics National Cancer Institute [[alternative HTML version deleted]]

On Wed, Nov 19, 2003 at 03:11:46PM -0500, Simon, Richard (NIH/NCI) wrote: > I'm running R 1.8 on a Windows XP professional box. > I tried to import a few U133 .cel files and run rma after downloading all > of the bioconductor packages. > > repdata <- ReadAffy() > eset <- rma(repdata) > > I first got a message that it autodownloaded hgu133atagcdf and that > installation was complete. > > Then I got an error in open.connection (con,"rb") unable to open connection > > Then I got a > > warning cannot open compressed file > 'C:/PROGRA~1/R/rw1080/library/hgu133atagcdf/data/hgu133atagcdf.rda > > Then > > error in library("hgu133atagcdf",lib.loc="C:PROGRA~1/R/rw1080/library") > .First.lib failed > > This is my first attempt to use bioconductor. I didn't get very far. Can > anyone suggest what is wrong? Hi, a little disagreement about who is supposed to unzip what, we should be able to fix this up on our end shortly. A "quick fix" on your end is to find the directory that the library is installed in C:/PROGRA~1/R/rw1080/library/hgu133atagcdf/data/ and in that directory you will find a file named Rdata.zip, if you unzip it, then all should be well (or at least you get past this error, I have no 133atag CEL files to see what one might need to do differently from that point on. Thanks for pointing this out (with enough detail to fix it), Robert > > Thanks, > > Rich Simon > > Richard Simon, D.Sc. > Chief, Biometric Research Branch > Head, Computational & Systems Biology Group > Division of Cancer Treatment & Diagnostics > National Cancer Institute > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+