An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070823/ 55310250/attachment.pl

"Martin O'Gorman" <martinogorman at="" yahoo.com=""> writes: > Hi there, I have just installed the "affy" package from bioconductor > by downloading the .zip file for windows and extracting to > ..\R\R-2.3.1\library\ ,ie the directory where all my R packages > live. However, I can't seem to open the package, getting the following > error message. > >> library(affy) Error in library(affy) : there is no package called > affy' > > I have followed the same procedure for affyio without any problems. Am > I doing something wrong? Actually, yes. Please follow the installation instructions here: http://www.bioconductor.org/download In R: source("http://bioconductor.org/biocLite.R") biocLite("affy") + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/

Hi Martin, Martin O'Gorman wrote: > Hi there, I have just installed the "affy" package from bioconductor > by downloading the .zip file for windows and extracting to > ..\R\R-2.3.1\library\ ,ie the directory where all my R packages live. > However, I can't seem to open the package, getting the following > error message. > >> library(affy) > Error in library(affy) : there is no package called 'affy' > > I have followed the same procedure for affyio without any problems. > Am I doing something wrong? Yep. You are doing things about as wrong as you possibly could (where did you get this idea?). You really shouldn't be downloading things directly, and you certainly shouldn't just be unzipping things in library directories. The preferred method is to use biocLite() to get things, as this function will a.) install things correctly, b.) get the correct version for the version of R you are using, and c.) get all other packages that the package you want depends on. source("http://www.bioconductor.org/biocLite.R") biocLite("affy") BTW, R-2.3.1 is pretty old; you should probably upgrade to 2.5.1 while you are at it. Best, Jim > > thanks Martin > > > > ____________________________________________________________________ ________________Ready > for the edge of your seat? > > > [[alternative HTML version deleted]] > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623

How about following the instructions in: http://www.bioconductor.org/docs/install-howto.html And everyone will suggest (emphatically) to update your R installation as well... Cei On Thu, 23 Aug 2007, Martin O'Gorman wrote: > Hi there, > I have just installed the "affy" package from bioconductor by downloading the .zip file for windows and extracting to ..\R\R-2.3.1\library\ ,ie the directory where all my R packages live. However, I can't seem to open the package, getting the following error message. > >> library(affy) > Error in library(affy) : there is no package called 'affy' > > I have followed the same procedure for affyio without any problems. Am I doing something wrong? > > thanks > Martin > > > > ____________________________________________________________________ ________________Ready for the edge of your seat? > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20070824/ 53c2bfb0/attachment.pl