Ah. Thanks Martin. Yes, that fixed it. Odd as I'd just compiled and installed this R instance to replace R 2.7.0, and installed all the BioC packages on Monday, so not sure how all the old packages ended up there... I think I used getBioC instead of biocLite but update.packages found a whole bunch of useful things to do - I guess that needs to be a part of the post configure/make/install dance in order to ensure any old cruft lying around is properly dealt with. I probably left off a sudo somewhere in the process, so the old system BioC packages were never actually overwritten.... <moral> update.packages might be helpful before composing help requests to the list... </moral> On Thu, Sep 24, 2009 at 9:12 AM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > Hi Ross -- affy and affyio are out of date relative to preprocessCore. > > source('http://bioconductor.org/biocLite.R') > old.packages(repos=biocinstallRepos()) > update.packages(repos=biocinstallRepos()) > > Martin > > Ross Lazarus wrote: > > While testing ArrayExpress with E-GEOD-17215 I see > > > > Error in rma(ae) : > > VECTOR_ELT() can only be applied to a 'list', not a 'character' > > > > being thrown by rma applied to the downloaded AffyBatch - shown below. > Not > > sure whether this is a problem with the source data at ArrayExpress or > > stupidity on my own part, but I can't find any sign of this specific > error > > text in any relevant google results - suggestions appreciated. R2.9.2 - > > sessionInfo() at end of post: > > > > ======================== > > R version 2.9.2 (2009-08-24) > > Copyright (C) 2009 The R Foundation for Statistical Computing > > ISBN 3-900051-07-0 > > > > R is free software and comes with ABSOLUTELY NO WARRANTY. > > You are welcome to redistribute it under certain conditions. > > Type 'license()' or 'licence()' for distribution details. > > > > Natural language support but running in an English locale > > > > R is a collaborative project with many contributors. > > Type 'contributors()' for more information and > > 'citation()' on how to cite R or R packages in publications. > > > > Type 'demo()' for some demos, 'help()' for on-line help, or > > 'help.start()' for an HTML browser interface to help. > > Type 'q()' to quit R. > > > > > >> library(ArrayExpress) > > Loading required package: Biobase > > > > Welcome to Bioconductor > > > > Vignettes contain introductory material. To view, type > > 'openVignette()'. To cite Bioconductor, see > > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > > > Loading required package: affy > > Loading required package: limma > > Loading required package: XML > >> ae = ArrayExpress('E-GEOD-17215',save=T) > > trying URL ' > > > ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/experiment/GEOD/E- GEOD-17215/E-GEOD-17215.raw.zip > > ' > > (----normal AE download stuff deleted-----) > > Read 48 items > > Read 48 items > >> ls() > > [1] "ae" "mapCdfName" > >> ae > > AffyBatch object > > size of arrays=744x744 features (10794 kb) > > cdf=HT_HG-U133A (22277 affyids) > > number of samples=6 > > number of genes=22277 > > annotation=hthgu133a > > notes= E-GEOD-17215 > > E-GEOD-17215 > > NA > > unknown_experiment_design_type > > NULL > >> rma(ae) > > Background correcting > > Normalizing > > Calculating Expression > > Error in rma(ae) : > > VECTOR_ELT() can only be applied to a 'list', not a 'character' > > > >> sessionInfo() > > R version 2.9.2 (2009-08-24) > > x86_64-unknown-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=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] hthgu133acdf_2.4.0 ArrayExpress_1.2.2 XML_1.99-0 > > limma_2.18.3 > > [5] affy_1.20.0 Biobase_2.4.1 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.10.1 preprocessCore_1.6.0 tools_2.9.2 > > > > > > ============== > > > > > -- > Martin Morgan > Computational Biology / Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. > PO Box 19024 Seattle, WA 98109 > > Location: Arnold Building M1 B861 > Phone: (206) 667-2793 > -- Ross Lazarus MBBS MPH Associate Professor, Department of Population Medicine; Director of Bioinformatics, Channing Laboratory 181 Longwood Ave., Boston MA 02115, USA. Tel: +617 525 2730 Fax: +617 525 0958 [[alternative HTML version deleted]]