you might also find the following useful: http://article.gmane.org/gmane.science.biology.informatics.conductor/ 12709/ b On Jun 20, 2007, at 10:54 PM, Aedin Culhane wrote: > Thanks Ben > I did use biocLite() to do the update, so this is surprising. affyiio > should have been installed as a dependency of affy. I used: > > source("http://www.bioconductor.org/biocLite.R") > biocLite() > > I just installed affyio manually and now it works fine. > > Thanks for your help > Aedin > > > Ben Bolstad wrote: >> You have a mismatch between your version of affy and your version of >> affyio. You need 1.4.0 or later (the version released with BioC2.0). >> >> As a general rule people should not be mixing and matching packages >> between different versions of BioC/R. It is always safest to re- >> install >> the release using biocLite() or getBioC() rather than trying to >> install >> packages manually and hoping it works. >> >> Best, >> >> Ben >> >> >> >> >> >> >> On Wed, 2007-06-20 at 19:38 -0400, aedin culhane wrote: >> >>> Hi BioC, >>> I am having problems getting ReadAffy to work on fc5. Any ideas? >>> Thanks. >>> Aedin >>> >>>> example(ReadAffy) >>> >>> RdAffy> if(require(affydata)){ >>> RdAffy+ celpath <- system.file("celfiles", package="affydata") >>> RdAffy+ fns <- list.celfiles(path=celpath,full.names=TRUE) >>> RdAffy+ >>> RdAffy+ cat("Reading files:\n",paste(fns,collapse="\n"),"\n") >>> RdAffy+ ##read a binary celfile >>> RdAffy+ abatch <- ReadAffy(filenames=fns[1]) >>> RdAffy+ ##read a text celfile >>> RdAffy+ abatch <- ReadAffy(filenames=fns[2]) >>> RdAffy+ ##read all files in that dir >>> RdAffy+ abatch <- ReadAffy(celfile.path=celpath) >>> RdAffy+ } >>> Loading required package: affydata >>> Reading files: >>> >>> /home/aedin/R/i686-redhat-linux-gnu-library/2.5/affydata/celfiles/ >>> binary.cel >>> /home/aedin/R/i686-redhat-linux-gnu-library/2.5/affydata/celfiles/ >>> text.cel >>> Error in read.affybatch(filenames = l$filenames, phenoData = l >>> $phenoData, : >>> VECTOR_ELT() can only be applied to a 'list', not a 'char' >>> >>> >>> >>>> sessionInfo() >>> R version 2.5.0 (2007-04-23) >>> i686-redhat-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ >>> US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGE >>> >>> S=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHO >>> NE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFI >>> CATION=C >>> >>> attached base packages: >>> [1] "tools" "stats" "graphics" "grDevices" "utils" >>> "datasets" >>> [7] "methods" "base" >>> >>> other attached packages: >>> affydata affy affyio Biobase >>> "1.11.2" "1.14.1" "1.0.0" "1.14.0" >>> >>> _______________________________________________ >>> 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 >>> > > > -- > Aed?n Culhane > Research Associate in Prof. J Quackenbush Lab > Harvard School of Public Health, Dana-Farber Cancer Institute > > 44 Binney Street, SM822 > Department of Biostatistics and Computational Biology, > Dana-Farber Cancer Institute > Boston, MA 02115 > USA > > Phone: +1 (617) 632 2468 > Fax: +1 (617) 582 7760 > Email: aedin at jimmy.harvard.edu > Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html > > _______________________________________________ > 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