[BioC] limma gene symbol not avialable problem

[Daofeng Li]

sorry to bother again
i installed the medicagoproble packages and tried again
the problem remains
and the output html report of limma have no DE gene part(blank)
hopes anyone could give a advice:)
Thanks again!

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(medicagocdf)
> library(medicagoprobe)
> library(affylmGUI)
Loading required package: limma
Loading required package: tcltk
Loading Tcl/Tk interface ... done

To begin, type affylmGUI()
> affylmGUI()

Searching for user-defined affylmGUI commands in
/usr/local/lib/R/library/affylmGUI/etc ...
> Loading required package: tkrplot

> Loading required package: xtable
Loading required package: R2HTML
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found
Error in get(x, envir, mode, inherits) : variable "HTMLenv" was not found

>
> 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=en_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.UTF-8;LC_IDENTIFICATION=C

attached base packages:
 [1] "tcltk"     "splines"   "tools"     "stats"     "graphics"  "grDevices"
 [7] "utils"     "datasets"  "methods"   "base"

other attached packages:
       R2HTML        xtable       tkrplot     affylmGUI         limma
       "1.58"       "1.4-6"      "0.0-16"      "1.10.2"      "2.10.5"
medicagoprobe   medicagocdf       affyPLM         gcrma   matchprobes
     "1.16.2"      "1.16.0"      "1.12.0"       "2.8.1"       "1.8.1"
     affydata          affy        affyio       Biobase
     "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(),
>



On 6/13/07, Daofeng Li <lidaof at gmail.com> 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?
> 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
>
> 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=en_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.UTF-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(),
> >
>
>
> --
> Daofeng Li
>


-- 
Daofeng Li