Hi Ben, The QC Assessment .pdf vignette of affyPLM seems to be missing from the latest windows binary. I just updated all my packages to make sure I wasn't missing anything. The vignette is still available on the bioC webpage (http://bioconductor.org/packages/release/bioc/vignettes/affyPLM/inst/ doc/QualityAssess.pdf) so I thought this must be a bug. Thanks, Jenny > source("http://bioconductor.org/biocLite.R") > update.packages(repos=biocinstallRepos(),ask=FALSE) trying URL 'http://bioconductor.org/packages/2.3/data/experiment/bin/windows/cont rib/2.8/affydata_1.11.4.zip' Content type 'application/zip' length 12730305 bytes (12.1 Mb) opened URL downloaded 12.1 Mb ### ... a bunch of packages being downloaded package 'affydata' successfully unpacked and MD5 sums checked package 'boot' successfully unpacked and MD5 sums checked package 'Category' successfully unpacked and MD5 sums checked package 'cluster' successfully unpacked and MD5 sums checked package 'foreign' successfully unpacked and MD5 sums checked package 'IRanges' successfully unpacked and MD5 sums checked package 'lattice' successfully unpacked and MD5 sums checked package 'mgcv' successfully unpacked and MD5 sums checked package 'nlme' successfully unpacked and MD5 sums checked package 'spam' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\drnevich\Local Settings\Temp\RtmpTGrSYa\downloaded_packages updating HTML package descriptions > > library(affyPLM) Loading required package: affy Loading required package: Biobase Loading required package: tools 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: gcrma Loading required package: matchprobes Loading required package: splines Loading required package: preprocessCore > openVignette() Please select a vignette: (entries marked by '[-]' have no PDF file) 1: affy - 1. Primer 2: affy - 2. Built-in Processing Methods 3: affy - 3. Custom Processing Methods 4: affy - 4. Import Methods 5: affyPLM - affyPLM: Advanced use of the MAplot function 6: affyPLM - affyPLM: Fitting Probe Level Models 7: affyPLM - affyPLM: the threestep function 8: Biobase - An introduction to Biobase and ExpressionSets 9: Biobase - Bioconductor Overview 10: Biobase - esApply Introduction 11: Biobase - Notes for eSet developers 12: Biobase - Notes for writing introductory 'how to' documents 13: Biobase - quick views of eSet instances 14: gcrma - gcrma1.2 15: matchprobes - Handling probe sequence information 16: affyPLM - affyPLM: Model Based QC Assessment of Affymetrix GeneChips [-] Selection: 16 Error in openVignette() : Sorry, no PDF file could be found for this vignette. Please reinstall the package with built vignettes. > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] affyPLM_1.18.1 preprocessCore_1.4.0 gcrma_2.14.1 [4] matchprobes_1.14.1 affy_1.20.2 Biobase_2.2.2 loaded via a namespace (and not attached): [1] affyio_1.10.1 > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu