[BioC] limma gene symbol not avialable problem

Daofeng Li lidaof at gmail.com
Wed Jun 13 04:48:34 CEST 2007

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?
is there any solution to fix that?Thanks!

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

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> 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)


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(),

Daofeng Li

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