[BioC] limma gene symbol not avialable problem

[James W. MacDonald]

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=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(),
> 
> 
> 


-- 
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


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