[BioC] Fwd: limma gene symbol not avialable problem

[Daofeng Li]

---------- Forwarded message ----------
From: Daofeng Li <lidaof at 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=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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>


--
Daofeng Li


-- 
Daofeng Li