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Question: limma gene symbol not avialable problem
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gravatar for lidaof
11.3 years ago by
lidaof450
United States
lidaof450 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
ADD COMMENTlink modified 11.3 years ago by James W. MacDonald47k • written 11.3 years ago by lidaof450
0
gravatar for James W. MacDonald
11.3 years ago by
United States
James W. MacDonald47k 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_U S.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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 11.3 years ago by James W. MacDonald47k
Hi Jim, sorry to disturb again but i really have no idea on how to make an anotation package for Medicago myself even after i have done some search with Google. is the CSV file u said available at http://www.affymetrix.com/support/technical/byproduct.affx?product=med icago i download the file "Medicago Annotations, CSV format (3.2 MB, 5/31/07)",but i dont know how to use it can you please give me some instructions to make that? Another fool question by me is that "package medicagocdf is not the annotation file?i cannot figout the difference between cdf file and anotation package you said" Thank anyone who waste time on this question:) Best Regards! Daofeng 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
ADD REPLYlink written 11.3 years ago by lidaof450
0
gravatar for lidaof
11.3 years ago by
lidaof450
United States
lidaof450 wrote:
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_U S.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
ADD COMMENTlink written 11.3 years ago by lidaof450
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