Hi, I'm getting a weird error when trying to load the affy package automatically during start-up using a .Rprofile file. The .Rprofile has only the following: library(RWinEdt) library(affy) When I put this .Rprofile in the same folder that Rgui.exe starts in (working directory) and start Rgui, everythings seems to load fine (see code 1 below), except that boxplot() and hist() seem to have lost their inherited methods for AffyBatch and exprSet objects. If I rename the .Rprofile to test.Rprofile so it won't automatically be sourced, but instead source it myself, boxplot() and hist() work fine (see code 2 below). If I change the .Rprofile so that the library(affy) is first, then I do get a error message upon loading (see code 3 below). Now, obviously a solution is to just manually source a file that has all the extra libraries and my own functions that I want to load each time, but I was wondering why it doesn't work to automatically work when using a .Rprofile file, and if this is a problem with the affy package or R instead. I should also mention that the same problems occur even if the .Rprofile file is: .First <- function() { library(RWinEdt) library(affy) } Thanks, Jenny CODE 1: (with .Rprofile in the working directory) R : Copyright 2005, The R Foundation for Statistical Computing Version 2.2.1 (2005-12-20 r36812) 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. Loading required package: methods Loading required package: utils Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. > raw.data <- ReadAffy() > hist(raw.data) Error in hist.default(raw.data) : 'x' must be numeric > boxplot(raw.data) Error in boxplot.default(raw.data) : 'names' attribute [12] must be the same length as the vector [0] > rma.data <- rma(raw.data) Background correcting Normalizing Calculating Expression > boxplot(rma.data) Error in boxplot.default(rma.data) : invalid first argument > raw.data AffyBatch object size of arrays=732x732 features (50240 kb) cdf=Canine (23913 affyids) number of samples=12 number of genes=23913 annotation=canine > rma.data Expression Set (exprSet) with 23913 genes 12 samples phenoData object with 1 variables and 12 cases varLabels sample: arbitrary numbering > sessionInfo() R version 2.2.1, 2005-12-20, i386-pc-mingw32 attached base packages: [1] "stats" "graphics" "grDevices" "datasets" "tools" "utils" [7] "methods" "base" other attached packages: caninecdf affy Biobase RWinEdt "1.10.0" "1.8.1" "1.8.0" "1.7-4" > CODE 2: (no .Rprofile in working directory) R : Copyright 2005, The R Foundation for Statistical Computing Version 2.2.1 (2005-12-20 r36812) 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. > source("test.Rprofile") Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, simply type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. > raw.data <- ReadAffy() > hist(raw.data) > boxplot(raw.data) > raw.data AffyBatch object size of arrays=732x732 features (50240 kb) cdf=Canine (23913 affyids) number of samples=12 number of genes=23913 annotation=canine > sessionInfo() R version 2.2.1, 2005-12-20, i386-pc-mingw32 attached base packages: [1] "tools" "methods" "stats" "graphics" "grDevices" "utils" [7] "datasets" "base" other attached packages: caninecdf affy Biobase RWinEdt "1.10.0" "1.8.1" "1.8.0" "1.7-4" > CODE 3: (using .Rprofile with library(affy) first) R : Copyright 2005, The R Foundation for Statistical Computing Version 2.2.1 (2005-12-20 r36812) 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. Loading required package: Biobase Loading required package: tools Loading required package: methods Welcome to Bioconductor Vignettes contain introductory material. To view, simply type 'openVignette()' or start with 'help(Biobase)'. For details on reading vignettes, see the openVignette help page. Error in inherits(x, "factor") : couldn't find function "winMenuNames" Error: .onLoad failed in 'loadNamespace' for 'Biobase' Error: package 'Biobase' could not be loaded > raw.data <- ReadAffy() Error: couldn't find function "ReadAffy" > sessionInfo() R version 2.2.1, 2005-12-20, i386-pc-mingw32 attached base packages: [1] "stats" "graphics" "grDevices" "utils" "datasets" "methods" [7] "tools" "base" > 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 uiuc.edu