---------- Forwarded message ---------- From: Daofeng Li <lidaof@gmail.com> Date: Jun 13, 2007 10:22 PM Subject: Re: [BioC] limma gene symbol not avialable problem To: "James W. MacDonald" <jmacdon at="" med.umich.edu=""> Hi Jim, Thank you so much for the information you provided. i will try to fix the problem...do some trying Thank you again:) Best Regards! On 6/13/07, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > Hi Daofeng, > > Daofeng Li wrote: > > Hi all, > > > > i am doing analysis with Affymetrix's Medicago GeneChip(TM) > > i use library(medicagocdf) without error > > when i try to use affylmGUI to draw a MA plot,i select use Gene > > Symbol,but limma told me Gene Symbol is not avialable.why this problem > > would occur? > > Because there is no annotation package for medicago. Without an > annotation package there is no mapping of probeset to gene symbol. > > > is there any solution to fix that?Thanks! > > You are going to have to annotate things yourself. Affy has an > annotation csv file that you could use to map from e.g., probe ID to > gene symbol (or whatever other annotation may exist in that file). > > Unfortunately something like medicago is likely to receive very little > attention because the user base is much smaller than say, the primate > chip types. Given the number of different chips (and platforms, for that > matter) and the finite resources of Bioconductor, we have to focus our > efforts where they will count the most. > > Because of this you will have to rely on your own resourcefulness to > figure out how things work and how to get what you want. This is both > the benefit and the curse of open source software - you have the ability > to do what you want with the code, but unlike proprietary software it's > often up to you to figure out what you want and how to get it. > > Best, > > Jim > > > > > > here is my code and sessioninfo: > > R version 2.5.0 (2007-04-23) > > Copyright (C) 2007 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(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: affyio > > > >>library(affyPLM) > > > > Loading required package: affydata > > Loading required package: gcrma > > Loading required package: matchprobes > > Loading required package: splines > > > >>library(affylmGUI) > > > > Loading required package: limma > > Loading required package: tcltk > > Loading Tcl/Tk interface ... done > > > > To begin, type affylmGUI() > > > >>library(medicagocdf) > >>affylmGUI() > > > > > > Searching for user-defined affylmGUI commands in > > /usr/local/lib/R/library/affylmGUI/etc ... > > > >>Loading required package: tkrplot > > > > > >>sessionInfo() > > > > R version 2.5.0 (2007-04-23) > > i686-pc-linux-gnu > > > > locale: > > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;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.U TF-8;LC_IDENTIFICATION=C > > > > attached base packages: > > [1] "tcltk" "splines" "tools" "stats" "graphics" "grDevices" > > [7] "utils" "datasets" "methods" "base" > > > > other attached packages: > > tkrplot medicagocdf affylmGUI limma affyPLM gcrma > > "0.0-16" "1.16.0" "1.10.2" "2.10.5" "1.12.0" "2.8.1" > > matchprobes affydata affy affyio Biobase > > "1.8.1" "1.11.2" "1.14.1" "1.4.0" "1.14.0" > > Warning messages: > > 1: package 'medicago' is not available in: install.packages(pkgs = > > cdfName, lib = .libPaths(), repos = Biobase::biocReposList(), > > 2: package 'medicago' is not available in: install.packages(pkgs = > > cdfName, lib = .libPaths(), repos = Biobase::biocReposList(), > > > > > > > > > -- > 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 > > > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues. > -- Daofeng Li -- Daofeng Li