Importing CDF file for custom array using makecdfenv
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Jenny Drnevich ★ 2.2k
@jenny-drnevich-382
Last seen 7.7 years ago
Hi Jim & others, I'm at my wit's end - I really cannot figure out anything I am doing wrong in trying to create an environment for a custom Affy array. It seems I'm having the same problem as in this thread, but the solution Jim suggested isn't working. I've followed the makecdfenv vignette, sections 3 and 4 (I'm following the advice to skip trying to make a package on a PC, for now). Here's what I've tried: R version 2.4.0 (2006-10-03) Copyright (C) 2006 The R Foundation for Statistical Computing ISBN 3-900051-07-0 #deleting most of intro > setwd("C:/Statistics/Clayton") > source("http://bioconductor.org/biocLite.R") > biocLite("makecdfenv") Running getBioC version 0.1.8 with R version 2.4.0 Running biocinstall version 1.9.9 with R version 2.4.0 Your version of R requires version 1.9 of Bioconductor. trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/mak ecdfenv_1.12.0.zip' Content type 'application/zip' length 3307506 bytes opened URL downloaded 3229Kb package 'makecdfenv' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\drnevich\Local Settings\Temp\RtmpCw5Rqb\downloaded_packages updating HTML package descriptions > library(makecdfenv) > cleancdfname(whatcdf("p0601_51.CEL")) Error in .Call("ReadHeader", filename, compress, PACKAGE = "affy") : C symbol name "ReadHeader" not in DLL for package "affy" I HOPE all the trouble I'm having below is related to this, and not to me! Because the 'whatcdf' isn't working, I tried to get the cdf name from an AffyBatch object: > raw <- ReadAffy() > raw at cdfName [1] "lund-zfa530237N" > cleancdfname(raw at cdfName) # the makecdf vignette says 'getCdfInfo' will look for an environment by this name for the AffyBatch [1] "lundzfa530237ncdf" > lundzfa530237ncdf <- make.cdf.env("lund-zfa530237N.cdf") Reading CDF file. Creating CDF environment Wait for about 231 dots.................................................................. ...................................................................... ...................................................................... ................. > length(ls(lundzfa530237ncdf)) #from the help file of 'make.cdf.env", so I think it's been created properly... [1] 23136 # ...but... > raw Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain lund-zfa530237N Library - package lundzfa530237ncdf not installed Data for package affy did not contain lundzfa530237ncdf Bioconductor - lundzfa530237ncdf not available AffyBatch object size of arrays=754x754 features (53306 kb) cdf=lund-zfa530237N (??? affyids) number of samples=12 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain lund-zfa530237N Library - package lundzfa530237ncdf not installed Data for package affy did not contain lundzfa530237ncdf Bioconductor - lundzfa530237ncdf not available In addition: Warning message: missing cdf environment ! in: show(<s4 object="" of="" class="" "affybatch"="">) I searched the archives and found this thread from Jim about the seemingly same error: >> I do not get any errors, but when I try to look at the affybatch object >> get the following message: >> >> Error in getCdfInfo(object) : Could not obtain CDF environment, problems >> encountered: >> specified environment does not contain XXX Library - package XXXcdf not >> installed Data for package affy did not contain XXXcdf Bioconductor - >> XXXcdf not available AffyBatch object size of arrays=291x291 features >> (15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in >> getCdfInfo(object) : Could not obtain CDF environment, problems >> encountered: >> Specified environment does not contain XXX > >This line is a hint, although rather oblique. When the affy package >looks for an environment in the current .GlobalEnv, it expects it to be >named XXX, so if you use make.cdf.env, you should name it XXX. OK, so this is contrary to what it says in the vignette, but I try it anyway: > rm(lundzfa530237ncdf) > lundzfa530237n <- make.cdf.env("lund-zfa530237N.cdf") Reading CDF file. Creating CDF environment Wait for about 231 dots.................................................................. ...................................................................... ...................................................................... ...................................... But still no luck! > raw Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain lund-zfa530237N Library - package lundzfa530237ncdf not installed Data for package affy did not contain lundzfa530237ncdf Bioconductor - lundzfa530237ncdf not available AffyBatch object size of arrays=754x754 features (53306 kb) cdf=lund-zfa530237N (??? affyids) number of samples=12 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain lund-zfa530237N Library - package lundzfa530237ncdf not installed Data for package affy did not contain lundzfa530237ncdf Bioconductor - lundzfa530237ncdf not available In addition: Warning message: missing cdf environment ! in: show(<s4 object="" of="" class="" "affybatch"="">) Am I doing anything wrong? I can't figure out what it could be for the life of me!!! Contents of workspace and sessionInfo below. Thanks, Jenny > ls() [1] "biocinstall" "biocinstall.affyPkgs" [3] "biocinstall.allPkgs" "biocinstall.defaultPkgs" [5] "biocinstall.graphPkgs" "biocinstall.litePkgs" [7] "biocinstall.monographPkgs" "biocLite" [9] "lundzfa530237n" "raw" > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: makecdfenv affyQCReport simpleaffy made4 scatterplot3d "1.12.0" "1.12.0" "2.8.0" "1.8.0" "0.3-24" ade4 affyPLM gcrma matchprobes affydata "1.4-2" "1.10.0" "2.6.0" "1.6.0" "1.10.0" affycoretools biomaRt RCurl XML GOstats "1.6.0" "1.8.0" "0.7-0" "0.99-93" "2.0.0" Category genefilter survival KEGG RBGL "2.0.0" "1.12.0" "2.29" "1.14.0" "1.10.0" annotate GO graph limma affy "1.12.0" "1.14.0" "1.12.0" "2.9.1" "1.12.0" affyio Biobase RWinEdt "1.2.0" "1.12.2" "1.7-5" > > > I do not get any errors, but when I try to look at the affybatch object > > I get the following message: > > > > Error in getCdfInfo(object) : Could not obtain CDF environment, problems > > encountered: > > Specified environment does not contain XXX Library - package XXXcdf not > > installed Data for package affy did not contain XXXcdf Bioconductor - > > XXXcdf not available AffyBatch object size of arrays=291x291 features > > (15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in > > getCdfInfo(object) : Could not obtain CDF environment, problems > > encountered: > > Specified environment does not contain XXX > >This line is a hint, although rather oblique. When the affy package >looks for an environment in the current .GlobalEnv, it expects it to be >named XXX, so if you use make.cdf.env, you should name it XXX. However, >if it looks for a package, it has to be named xxxcdf. The best bet is to >allow make.cdf.package to do the package naming itself, because it will >be 100% correct. > > > > > I have tried putting the CDF file (created by BioC) in the R libraries > > folder with other libraries, but no luck. > >Nope. You have to install. This would have worked for maybe R-1.7.0 or >so, but modern versions of R require you to install the right way. > >HTH, > >Jim > > > > > In the makecdfenv vignette it says to "open a terminal with an operating > > system shell and write R CMD INSTALL XXXcdf", but I don't know how to do > > this on windows. > > > > Any suggestions would be greatly appreciated! > > > > Ann > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -------------------------------------------------------- > > > > > > This email is confidential and intended solely for the use o...{{dropped}} > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > >-- >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. > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
Microarray GO Survival Cancer cdf Biobase annotate genefilter affy graph makecdfenv GO • 1.0k views
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@kasper-daniel-hansen-2979
Last seen 10 months ago
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On Nov 8, 2006, at 2:49 PM, Jenny Drnevich wrote: > Hi Jim & others, > > I'm at my wit's end - I really cannot figure out anything I am > doing wrong > in trying to create an environment for a custom Affy array. It > seems I'm > having the same problem as in this thread, but the solution Jim > suggested > isn't working. I've followed the makecdfenv vignette, sections 3 > and 4 (I'm > following the advice to skip trying to make a package on a PC, for > now). > Here's what I've tried: > > > R version 2.4.0 (2006-10-03) > Copyright (C) 2006 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > #deleting most of intro > >> setwd("C:/Statistics/Clayton") > >> source("http://bioconductor.org/biocLite.R") > >> biocLite("makecdfenv") > > Running getBioC version 0.1.8 with R version 2.4.0 > Running biocinstall version 1.9.9 with R version 2.4.0 > Your version of R requires version 1.9 of Bioconductor. > trying URL > 'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/ > makecdfenv_1.12.0.zip' > Content type 'application/zip' length 3307506 bytes > opened URL > downloaded 3229Kb > > package 'makecdfenv' successfully unpacked and MD5 sums checked > > The downloaded packages are in > C:\Documents and Settings\drnevich\Local > Settings\Temp\RtmpCw5Rqb\downloaded_packages > updating HTML package descriptions > >> library(makecdfenv) > >> cleancdfname(whatcdf("p0601_51.CEL")) > > Error in .Call("ReadHeader", filename, compress, PACKAGE = "affy") : > C symbol name "ReadHeader" not in DLL for package "affy" This seems to be a bug in whatcdf: now all the IO routines have been moved to affyio, so the .Call has to be ..., PACKAGE = "affyio". CC'ed to the maintainer. > > I HOPE all the trouble I'm having below is related to this, and not > to me! > Because the 'whatcdf' isn't working, I tried to get the cdf name > from an > AffyBatch object: > >> raw <- ReadAffy() > >> raw at cdfName > [1] "lund-zfa530237N" > >> cleancdfname(raw at cdfName) # the makecdf vignette says >> 'getCdfInfo' will > look for an environment by this name for the AffyBatch > [1] "lundzfa530237ncdf" > >> lundzfa530237ncdf <- make.cdf.env("lund-zfa530237N.cdf") > Reading CDF file. > Creating CDF environment > Wait for about 231 > dots.................................................................. > ...................................................................... > ...................................................................... > ................. > >> length(ls(lundzfa530237ncdf)) #from the help file of >> 'make.cdf.env", so > I think it's been created properly... > [1] 23136 > > # ...but... >> raw > Error in getCdfInfo(object) : Could not obtain CDF environment, > problems > encountered: > Specified environment does not contain lund-zfa530237N > Library - package lundzfa530237ncdf not installed > Data for package affy did not contain lundzfa530237ncdf > Bioconductor - lundzfa530237ncdf not available > AffyBatch object > size of arrays=754x754 features (53306 kb) > cdf=lund-zfa530237N (??? affyids) > number of samples=12 > Error in getCdfInfo(object) : Could not obtain CDF environment, > problems > encountered: > Specified environment does not contain lund-zfa530237N > Library - package lundzfa530237ncdf not installed > Data for package affy did not contain lundzfa530237ncdf > Bioconductor - lundzfa530237ncdf not available > In addition: Warning message: > missing cdf environment ! in: show(<s4 object="" of="" class="" "affybatch"="">) > > I searched the archives and found this thread from Jim about the > seemingly > same error: > >>> I do not get any errors, but when I try to look at the affybatch >>> object >>> get the following message: >>> >>> Error in getCdfInfo(object) : Could not obtain CDF environment, >>> problems >>> encountered: >>> specified environment does not contain XXX Library - package >>> XXXcdf not >>> installed Data for package affy did not contain XXXcdf >>> Bioconductor - >>> XXXcdf not available AffyBatch object size of arrays=291x291 >>> features >>> (15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in >>> getCdfInfo(object) : Could not obtain CDF environment, problems >>> encountered: >>> Specified environment does not contain XXX >> >> This line is a hint, although rather oblique. When the affy package >> looks for an environment in the current .GlobalEnv, it expects it >> to be >> named XXX, so if you use make.cdf.env, you should name it XXX. > > OK, so this is contrary to what it says in the vignette, but I try > it anyway: > >> rm(lundzfa530237ncdf) >> lundzfa530237n <- make.cdf.env("lund-zfa530237N.cdf") > Reading CDF file. > Creating CDF environment > Wait for about 231 > dots.................................................................. > ...................................................................... > ...................................................................... > ...................................... > > But still no luck! > >> raw > Error in getCdfInfo(object) : Could not obtain CDF environment, > problems > encountered: > Specified environment does not contain lund-zfa530237N > Library - package lundzfa530237ncdf not installed > Data for package affy did not contain lundzfa530237ncdf > Bioconductor - lundzfa530237ncdf not available > AffyBatch object > size of arrays=754x754 features (53306 kb) > cdf=lund-zfa530237N (??? affyids) > number of samples=12 > Error in getCdfInfo(object) : Could not obtain CDF environment, > problems > encountered: > Specified environment does not contain lund-zfa530237N > Library - package lundzfa530237ncdf not installed > Data for package affy did not contain lundzfa530237ncdf > Bioconductor - lundzfa530237ncdf not available > In addition: Warning message: > missing cdf environment ! in: show(<s4 object="" of="" class="" "affybatch"="">) > > Am I doing anything wrong? I can't figure out what it could be for > the life > of me!!! Contents of workspace and sessionInfo below. If you look at the error message it seems you have a capitalization issue - it seems as if the package is supposed to be called XXXncdf (without "-"), but the environment is supposed to be called XXXN (with "-"). However, my own experiences with makecdfenv and CDF names are limited... Kasper > Thanks, > Jenny > > > >> ls() > [1] "biocinstall" "biocinstall.affyPkgs" > [3] "biocinstall.allPkgs" "biocinstall.defaultPkgs" > [5] "biocinstall.graphPkgs" "biocinstall.litePkgs" > [7] "biocinstall.monographPkgs" "biocLite" > [9] "lundzfa530237n" "raw" > >> sessionInfo() > R version 2.4.0 (2006-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" > "grDevices" > [7] "utils" "datasets" "base" > > other attached packages: > makecdfenv affyQCReport simpleaffy made4 scatterplot3d > "1.12.0" "1.12.0" "2.8.0" "1.8.0" "0.3-24" > ade4 affyPLM gcrma matchprobes affydata > "1.4-2" "1.10.0" "2.6.0" "1.6.0" "1.10.0" > affycoretools biomaRt RCurl XML GOstats > "1.6.0" "1.8.0" "0.7-0" "0.99-93" "2.0.0" > Category genefilter survival KEGG RBGL > "2.0.0" "1.12.0" "2.29" "1.14.0" "1.10.0" > annotate GO graph limma affy > "1.12.0" "1.14.0" "1.12.0" "2.9.1" "1.12.0" > affyio Biobase RWinEdt > "1.2.0" "1.12.2" "1.7-5" >> > > > > >>> I do not get any errors, but when I try to look at the affybatch >>> object >>> I get the following message: >>> >>> Error in getCdfInfo(object) : Could not obtain CDF environment, >>> problems >>> encountered: >>> Specified environment does not contain XXX Library - package >>> XXXcdf not >>> installed Data for package affy did not contain XXXcdf >>> Bioconductor - >>> XXXcdf not available AffyBatch object size of arrays=291x291 >>> features >>> (15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in >>> getCdfInfo(object) : Could not obtain CDF environment, problems >>> encountered: >>> Specified environment does not contain XXX >> >> This line is a hint, although rather oblique. When the affy package >> looks for an environment in the current .GlobalEnv, it expects it >> to be >> named XXX, so if you use make.cdf.env, you should name it XXX. >> However, >> if it looks for a package, it has to be named xxxcdf. The best bet >> is to >> allow make.cdf.package to do the package naming itself, because it >> will >> be 100% correct. >> >>> >>> I have tried putting the CDF file (created by BioC) in the R >>> libraries >>> folder with other libraries, but no luck. >> >> Nope. You have to install. This would have worked for maybe >> R-1.7.0 or >> so, but modern versions of R require you to install the right way. >> >> HTH, >> >> Jim >> >>> >>> In the makecdfenv vignette it says to "open a terminal with an >>> operating >>> system shell and write R CMD INSTALL XXXcdf", but I don't know >>> how to do >>> this on windows. >>> >>> Any suggestions would be greatly appreciated! >>> >>> Ann >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> -------------------------------------------------------- >>> >>> >>> This email is confidential and intended solely for the use o... >>> {{dropped}} >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> -- >> 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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
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@james-w-macdonald-5106
Last seen 4 hours ago
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Hi Jenny, Jenny Drnevich wrote: > Hi Jim & others, > > I'm at my wit's end - I really cannot figure out anything I am doing wrong > in trying to create an environment for a custom Affy array. It seems I'm > having the same problem as in this thread, but the solution Jim suggested > isn't working. I've followed the makecdfenv vignette, sections 3 and 4 (I'm > following the advice to skip trying to make a package on a PC, for now). > Here's what I've tried: > > > R version 2.4.0 (2006-10-03) > Copyright (C) 2006 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > #deleting most of intro > > > setwd("C:/Statistics/Clayton") > > > source("http://bioconductor.org/biocLite.R") > > > biocLite("makecdfenv") > > Running getBioC version 0.1.8 with R version 2.4.0 > Running biocinstall version 1.9.9 with R version 2.4.0 > Your version of R requires version 1.9 of Bioconductor. > trying URL > 'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/m akecdfenv_1.12.0.zip' > Content type 'application/zip' length 3307506 bytes > opened URL > downloaded 3229Kb > > package 'makecdfenv' successfully unpacked and MD5 sums checked > > The downloaded packages are in > C:\Documents and Settings\drnevich\Local > Settings\Temp\RtmpCw5Rqb\downloaded_packages > updating HTML package descriptions > > > library(makecdfenv) > > > cleancdfname(whatcdf("p0601_51.CEL")) > > Error in .Call("ReadHeader", filename, compress, PACKAGE = "affy") : > C symbol name "ReadHeader" not in DLL for package "affy" That's an odd one. The error here is because 'ReadHeader' isn't in affy anymore, it's in affyio. I was positive these had all been changed. I will get this fixed tomorrow, and into the release repository. > > > I HOPE all the trouble I'm having below is related to this, and not to me! > Because the 'whatcdf' isn't working, I tried to get the cdf name from an > AffyBatch object: > > > raw <- ReadAffy() > > > raw at cdfName > [1] "lund-zfa530237N" Note here what the cdfname is. The affy package will look for this *exact* name when looking for the environment. Below, you call it something else: > lundzfa530237n <- make.cdf.env("lund-zfa530237N.cdf") If you name it lund-zfa530237N, then everything should be copacetic. I know this is a PITA. Seth looked at making the naming consistent around the time I wrote the email you quote below, and for some reason (I forget now what it was) fixing it was way more difficult than one might think it would be, especially considering that it is not very common to use an unpackaged environment. Have you considered making a cdf package? Using an env is OK, but it isn't as persistent as a package would be (plus you will automatically get the correct name using make.cdf.package()). HTH, Jim > > > cleancdfname(raw at cdfName) # the makecdf vignette says 'getCdfInfo' will > look for an environment by this name for the AffyBatch > [1] "lundzfa530237ncdf" > > > lundzfa530237ncdf <- make.cdf.env("lund-zfa530237N.cdf") > Reading CDF file. > Creating CDF environment > Wait for about 231 > dots................................................................ ...................................................................... ...................................................................... ................... > > > length(ls(lundzfa530237ncdf)) #from the help file of 'make.cdf.env", so > I think it's been created properly... > [1] 23136 > > # ...but... > > raw > Error in getCdfInfo(object) : Could not obtain CDF environment, problems > encountered: > Specified environment does not contain lund-zfa530237N > Library - package lundzfa530237ncdf not installed > Data for package affy did not contain lundzfa530237ncdf > Bioconductor - lundzfa530237ncdf not available > AffyBatch object > size of arrays=754x754 features (53306 kb) > cdf=lund-zfa530237N (??? affyids) > number of samples=12 > Error in getCdfInfo(object) : Could not obtain CDF environment, problems > encountered: > Specified environment does not contain lund-zfa530237N > Library - package lundzfa530237ncdf not installed > Data for package affy did not contain lundzfa530237ncdf > Bioconductor - lundzfa530237ncdf not available > In addition: Warning message: > missing cdf environment ! in: show(<s4 object="" of="" class="" "affybatch"="">) > > I searched the archives and found this thread from Jim about the seemingly > same error: > > >> I do not get any errors, but when I try to look at the affybatch object > >> get the following message: > >> > >> Error in getCdfInfo(object) : Could not obtain CDF environment, problems > >> encountered: > >> specified environment does not contain XXX Library - package XXXcdf not > >> installed Data for package affy did not contain XXXcdf Bioconductor - > >> XXXcdf not available AffyBatch object size of arrays=291x291 features > >> (15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in > >> getCdfInfo(object) : Could not obtain CDF environment, problems > >> encountered: > >> Specified environment does not contain XXX > > > >This line is a hint, although rather oblique. When the affy package > >looks for an environment in the current .GlobalEnv, it expects it to be > >named XXX, so if you use make.cdf.env, you should name it XXX. > > OK, so this is contrary to what it says in the vignette, but I try it anyway: > > > rm(lundzfa530237ncdf) > > lundzfa530237n <- make.cdf.env("lund-zfa530237N.cdf") > Reading CDF file. > Creating CDF environment > Wait for about 231 > dots................................................................ ...................................................................... ...................................................................... ........................................ > > But still no luck! > > > raw > Error in getCdfInfo(object) : Could not obtain CDF environment, problems > encountered: > Specified environment does not contain lund-zfa530237N > Library - package lundzfa530237ncdf not installed > Data for package affy did not contain lundzfa530237ncdf > Bioconductor - lundzfa530237ncdf not available > AffyBatch object > size of arrays=754x754 features (53306 kb) > cdf=lund-zfa530237N (??? affyids) > number of samples=12 > Error in getCdfInfo(object) : Could not obtain CDF environment, problems > encountered: > Specified environment does not contain lund-zfa530237N > Library - package lundzfa530237ncdf not installed > Data for package affy did not contain lundzfa530237ncdf > Bioconductor - lundzfa530237ncdf not available > In addition: Warning message: > missing cdf environment ! in: show(<s4 object="" of="" class="" "affybatch"="">) > > Am I doing anything wrong? I can't figure out what it could be for the life > of me!!! Contents of workspace and sessionInfo below. > > Thanks, > Jenny > > > > > ls() > [1] "biocinstall" "biocinstall.affyPkgs" > [3] "biocinstall.allPkgs" "biocinstall.defaultPkgs" > [5] "biocinstall.graphPkgs" "biocinstall.litePkgs" > [7] "biocinstall.monographPkgs" "biocLite" > [9] "lundzfa530237n" "raw" > > > sessionInfo() > R version 2.4.0 (2006-10-03) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" > [7] "utils" "datasets" "base" > > other attached packages: > makecdfenv affyQCReport simpleaffy made4 scatterplot3d > "1.12.0" "1.12.0" "2.8.0" "1.8.0" "0.3-24" > ade4 affyPLM gcrma matchprobes affydata > "1.4-2" "1.10.0" "2.6.0" "1.6.0" "1.10.0" > affycoretools biomaRt RCurl XML GOstats > "1.6.0" "1.8.0" "0.7-0" "0.99-93" "2.0.0" > Category genefilter survival KEGG RBGL > "2.0.0" "1.12.0" "2.29" "1.14.0" "1.10.0" > annotate GO graph limma affy > "1.12.0" "1.14.0" "1.12.0" "2.9.1" "1.12.0" > affyio Biobase RWinEdt > "1.2.0" "1.12.2" "1.7-5" > > > > > > >>>I do not get any errors, but when I try to look at the affybatch object >>>I get the following message: >>> >>>Error in getCdfInfo(object) : Could not obtain CDF environment, problems >>>encountered: >>>Specified environment does not contain XXX Library - package XXXcdf not >>>installed Data for package affy did not contain XXXcdf Bioconductor - >>>XXXcdf not available AffyBatch object size of arrays=291x291 features >>>(15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in >>>getCdfInfo(object) : Could not obtain CDF environment, problems >>>encountered: >>>Specified environment does not contain XXX >> >>This line is a hint, although rather oblique. When the affy package >>looks for an environment in the current .GlobalEnv, it expects it to be >>named XXX, so if you use make.cdf.env, you should name it XXX. However, >>if it looks for a package, it has to be named xxxcdf. The best bet is to >>allow make.cdf.package to do the package naming itself, because it will >>be 100% correct. >> >> >>>I have tried putting the CDF file (created by BioC) in the R libraries >>>folder with other libraries, but no luck. >> >>Nope. You have to install. This would have worked for maybe R-1.7.0 or >>so, but modern versions of R require you to install the right way. >> >>HTH, >> >>Jim >> >> >>>In the makecdfenv vignette it says to "open a terminal with an operating >>>system shell and write R CMD INSTALL XXXcdf", but I don't know how to do >>>this on windows. >>> >>>Any suggestions would be greatly appreciated! >>> >>>Ann >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor at stat.math.ethz.ch >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>>Search the archives: >>>http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>>-------------------------------------------------------- >>> >>> >>>This email is confidential and intended solely for the use o...{{dropped}} >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor at stat.math.ethz.ch >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>>Search the archives: >> >>http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >>-- >>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. >> >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: >>http://news.gmane.org/gmane.science.biology.informatics.conductor > > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at uiuc.edu > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive 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.
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Hi all, Thanks Jim and Kasper for your responses. I'm still having trouble, and I have a suggestion for changing the makecdfenv vignette... >>I HOPE all the trouble I'm having below is related to this, and not to >>me! Because the 'whatcdf' isn't working, I tried to get the cdf name from >>an AffyBatch object: >> > raw <- ReadAffy() >> > raw at cdfName >>[1] "lund-zfa530237N" > >Note here what the cdfname is. The affy package will look for this *exact* >name when looking for the environment. Below, you call it something else: > > > lundzfa530237n <- make.cdf.env("lund-zfa530237N.cdf") > >If you name it lund-zfa530237N, then everything should be copacetic. The reason I tried naming it "lundzfa530237ncdf" and then "lundzfa530237n", not "lund-zfa530237N" is because the vignette, under Section 4, Naming of CDF Packages and Environments, specifically says: "The method getCdfInfo takes as an argument AffyBatch and returns the appropriate environment. If x is an AffyBatch, this function will look for an environment with name cleancdfname(x at cdfName)." Perhaps this should be changed? At any rate, I tried naming it "lund-zfa530237N", but the "-" in the name is messing everything up: > raw at cdfName [1] "lund-zfa530237N" > lund-zfa530237N <- make.cdf.env("lund-zfa530237N.cdf") Reading CDF file. Creating CDF environment Wait for about 231 dots.................................................................. ...................................................................... ...................................................................... .............................. Error in lund - zfa530237N <- make.cdf.env("lund-zfa530237N.cdf") : object "lund" not found > length(ls(lund-zfa530237N)) Error in try(name) : object "lund" not found Error in as.environment(pos) : no item called "lund - zfa530237N" on the search list So I decided just to change raw at cdfName to "lundzfa530237n" as a work around for now. I probably won't be seeing any more experiments using this custom array, although I would like to make a cdf package for it. That's another long story... I thought I had everything needed because I had compiled some code successfully with R 2.3.0, but I'm not able to make the cdf package. We're installing R on our new blade system next week, so I'll just wait for that! Thanks, Jenny >I know this is a PITA. Seth looked at making the naming consistent around >the time I wrote the email you quote below, and for some reason (I forget >now what it was) fixing it was way more difficult than one might think it >would be, especially considering that it is not very common to use an >unpackaged environment. > >Have you considered making a cdf package? Using an env is OK, but it isn't >as persistent as a package would be (plus you will automatically get the >correct name using make.cdf.package()). > > >HTH, > >Jim > > >> > cleancdfname(raw at cdfName) # the makecdf vignette says 'getCdfInfo' >> will look for an environment by this name for the AffyBatch >>[1] "lundzfa530237ncdf" >> > lundzfa530237ncdf <- make.cdf.env("lund-zfa530237N.cdf") >>Reading CDF file. >>Creating CDF environment >>Wait for about 231 >>dots................................................................ ...................................................................... ...................................................................... ................... >> > length(ls(lundzfa530237ncdf)) #from the help file of 'make.cdf.env", >> so I think it's been created properly... >>[1] 23136 >># ...but... >> > raw >>Error in getCdfInfo(object) : Could not obtain CDF environment, problems >>encountered: >>Specified environment does not contain lund-zfa530237N >>Library - package lundzfa530237ncdf not installed >>Data for package affy did not contain lundzfa530237ncdf >>Bioconductor - lundzfa530237ncdf not available >>AffyBatch object >>size of arrays=754x754 features (53306 kb) >>cdf=lund-zfa530237N (??? affyids) >>number of samples=12 >>Error in getCdfInfo(object) : Could not obtain CDF environment, problems >>encountered: >>Specified environment does not contain lund-zfa530237N >>Library - package lundzfa530237ncdf not installed >>Data for package affy did not contain lundzfa530237ncdf >>Bioconductor - lundzfa530237ncdf not available >>In addition: Warning message: >>missing cdf environment ! in: show(<s4 object="" of="" class="" "affybatch"="">) >>I searched the archives and found this thread from Jim about the >>seemingly same error: >> >> I do not get any errors, but when I try to look at the affybatch object >> >> get the following message: >> >> >> >> Error in getCdfInfo(object) : Could not obtain CDF environment, problems >> >> encountered: >> >> specified environment does not contain XXX Library - package XXXcdf not >> >> installed Data for package affy did not contain XXXcdf Bioconductor - >> >> XXXcdf not available AffyBatch object size of arrays=291x291 features >> >> (15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in >> >> getCdfInfo(object) : Could not obtain CDF environment, problems >> >> encountered: >> >> Specified environment does not contain XXX >> > >> >This line is a hint, although rather oblique. When the affy package >> >looks for an environment in the current .GlobalEnv, it expects it to be >> >named XXX, so if you use make.cdf.env, you should name it XXX. >>OK, so this is contrary to what it says in the vignette, but I try it anyway: >> > rm(lundzfa530237ncdf) >> > lundzfa530237n <- make.cdf.env("lund-zfa530237N.cdf") >>Reading CDF file. >>Creating CDF environment >>Wait for about 231 >>dots................................................................ ...................................................................... ...................................................................... ........................................ >>But still no luck! >> > raw >>Error in getCdfInfo(object) : Could not obtain CDF environment, problems >>encountered: >>Specified environment does not contain lund-zfa530237N >>Library - package lundzfa530237ncdf not installed >>Data for package affy did not contain lundzfa530237ncdf >>Bioconductor - lundzfa530237ncdf not available >>AffyBatch object >>size of arrays=754x754 features (53306 kb) >>cdf=lund-zfa530237N (??? affyids) >>number of samples=12 >>Error in getCdfInfo(object) : Could not obtain CDF environment, problems >>encountered: >>Specified environment does not contain lund-zfa530237N >>Library - package lundzfa530237ncdf not installed >>Data for package affy did not contain lundzfa530237ncdf >>Bioconductor - lundzfa530237ncdf not available >>In addition: Warning message: >>missing cdf environment ! in: show(<s4 object="" of="" class="" "affybatch"="">) >>Am I doing anything wrong? I can't figure out what it could be for the >>life of me!!! Contents of workspace and sessionInfo below. >>Thanks, >>Jenny >> >> > ls() >> [1] "biocinstall" "biocinstall.affyPkgs" >> [3] "biocinstall.allPkgs" "biocinstall.defaultPkgs" >> [5] "biocinstall.graphPkgs" "biocinstall.litePkgs" >> [7] "biocinstall.monographPkgs" "biocLite" >> [9] "lundzfa530237n" "raw" >> > sessionInfo() >>R version 2.4.0 (2006-10-03) >>i386-pc-mingw32 >>locale: >>LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>States.1252;LC_MONETARY=English_United >>States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>attached base packages: >>[1] "splines" "tools" "methods" "stats" "graphics" "grDevices" >>[7] "utils" "datasets" "base" >>other attached packages: >> makecdfenv affyQCReport simpleaffy made4 scatterplot3d >> "1.12.0" "1.12.0" "2.8.0" "1.8.0" "0.3-24" >> ade4 affyPLM gcrma matchprobes affydata >> "1.4-2" "1.10.0" "2.6.0" "1.6.0" "1.10.0" >>affycoretools biomaRt RCurl XML GOstats >> "1.6.0" "1.8.0" "0.7-0" "0.99-93" "2.0.0" >> Category genefilter survival KEGG RBGL >> "2.0.0" "1.12.0" "2.29" "1.14.0" "1.10.0" >> annotate GO graph limma affy >> "1.12.0" "1.14.0" "1.12.0" "2.9.1" "1.12.0" >> affyio Biobase RWinEdt >> "1.2.0" "1.12.2" "1.7-5" >> > >> >> >>>>I do not get any errors, but when I try to look at the affybatch object >>>>I get the following message: >>>> >>>>Error in getCdfInfo(object) : Could not obtain CDF environment, problems >>>>encountered: >>>>Specified environment does not contain XXX Library - package XXXcdf not >>>>installed Data for package affy did not contain XXXcdf Bioconductor - >>>>XXXcdf not available AffyBatch object size of arrays=291x291 features >>>>(15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in >>>>getCdfInfo(object) : Could not obtain CDF environment, problems >>>>encountered: >>>>Specified environment does not contain XXX >>> >>>This line is a hint, although rather oblique. When the affy package >>>looks for an environment in the current .GlobalEnv, it expects it to be >>>named XXX, so if you use make.cdf.env, you should name it XXX. However, >>>if it looks for a package, it has to be named xxxcdf. The best bet is to >>>allow make.cdf.package to do the package naming itself, because it will >>>be 100% correct. >>> >>> >>>>I have tried putting the CDF file (created by BioC) in the R libraries >>>>folder with other libraries, but no luck. >>> >>>Nope. You have to install. This would have worked for maybe R-1.7.0 or >>>so, but modern versions of R require you to install the right way. >>> >>>HTH, >>> >>>Jim >>> >>> >>>>In the makecdfenv vignette it says to "open a terminal with an operating >>>>system shell and write R CMD INSTALL XXXcdf", but I don't know how to do >>>>this on windows. >>>> >>>>Any suggestions would be greatly appreciated! >>>> >>>>Ann >>>> >>>>_______________________________________________ >>>>Bioconductor mailing list >>>>Bioconductor at stat.math.ethz.ch >>>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>Search the archives: >>>>http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>>-------------------------------------------------------- >>>> >>>> >>>>This email is confidential and intended solely for the use o...{{dropped}} >>>> >>>>_______________________________________________ >>>>Bioconductor mailing list >>>>Bioconductor at stat.math.ethz.ch >>>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>Search the archives: >>> >>>http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> >>>-- >>>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. >>> >>>_______________________________________________ >>>Bioconductor mailing list >>>Bioconductor at stat.math.ethz.ch >>>https://stat.ethz.ch/mailman/listinfo/bioconductor >>>Search the archives: >>>http://news.gmane.org/gmane.science.biology.informatics.conductor >> >>Jenny Drnevich, Ph.D. >>Functional Genomics Bioinformatics Specialist >>W.M. Keck Center for Comparative and Functional Genomics >>Roy J. Carver Biotechnology Center >>University of Illinois, Urbana-Champaign >>330 ERML >>1201 W. Gregory Dr. >>Urbana, IL 61801 >>USA >>ph: 217-244-7355 >>fax: 217-265-5066 >>e-mail: drnevich at uiuc.edu >>_______________________________________________ >>Bioconductor mailing list >>Bioconductor at stat.math.ethz.ch >>https://stat.ethz.ch/mailman/listinfo/bioconductor >>Search the archives: >>http://news.gmane.org/gmane.science.biology.informatics.conductor > > >-- >James W. MacDonald >University of Michigan >Affymetrix and cDNA Microarray Core >1500 E Medical Center Drive >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. Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu
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Jenny Drnevich wrote: > Hi all, > > Thanks Jim and Kasper for your responses. I'm still having trouble, and > I have a suggestion for changing the makecdfenv vignette... > >>> I HOPE all the trouble I'm having below is related to this, and not >>> to me! Because the 'whatcdf' isn't working, I tried to get the cdf >>> name from an AffyBatch object: >>> > raw <- ReadAffy() >>> > raw at cdfName >>> [1] "lund-zfa530237N" >> >> >> Note here what the cdfname is. The affy package will look for this >> *exact* name when looking for the environment. Below, you call it >> something else: >> >> > lundzfa530237n <- make.cdf.env("lund-zfa530237N.cdf") >> >> If you name it lund-zfa530237N, then everything should be copacetic. > > > The reason I tried naming it "lundzfa530237ncdf" and then > "lundzfa530237n", not "lund-zfa530237N" is because the vignette, under > Section 4, Naming of CDF Packages and Environments, specifically says: > > "The method getCdfInfo takes as an argument AffyBatch and returns the > appropriate environment. If x is an AffyBatch, this function will look > for an environment with name cleancdfname(x at cdfName)." > > Perhaps this should be changed? At any rate, I tried naming it > "lund-zfa530237N", but the "-" in the name is messing everything up: Good point. The reason for the cleancdfname() function is to get rid of cruft like the "-" which will create the error you saw below. I will make some changes to the vignette that will hopefully make this clearer, and give a reasonable work around for situations like this. Thanks for your input. Best, Jim -- 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.
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Hi Jenny, I had same problem few month ago. You could solve this problem by doing like: > lundzfa530237ncdf <- make.cdf.env("lund-zfa530237N.cdf") > Data <- ReadAffy() > Data at cdfName <- " lundzfa530237ncdf" This worked for me. Sung-Chur Sim Postdoctoral Researcher Ohio State University, OARDC 1680 Madison Ave. Wooster, OH 44691 -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Jenny Drnevich Sent: Wednesday, November 08, 2006 5:49 PM To: James W. MacDonald Cc: BioConductor Mail List Subject: Re: [BioC] Importing CDF file for custom array using makecdfenv Hi Jim & others, I'm at my wit's end - I really cannot figure out anything I am doing wrong in trying to create an environment for a custom Affy array. It seems I'm having the same problem as in this thread, but the solution Jim suggested isn't working. I've followed the makecdfenv vignette, sections 3 and 4 (I'm following the advice to skip trying to make a package on a PC, for now). Here's what I've tried: R version 2.4.0 (2006-10-03) Copyright (C) 2006 The R Foundation for Statistical Computing ISBN 3-900051-07-0 #deleting most of intro > setwd("C:/Statistics/Clayton") > source("http://bioconductor.org/biocLite.R") > biocLite("makecdfenv") Running getBioC version 0.1.8 with R version 2.4.0 Running biocinstall version 1.9.9 with R version 2.4.0 Your version of R requires version 1.9 of Bioconductor. trying URL 'http://bioconductor.org/packages/1.9/bioc/bin/windows/contrib/2.4/mak ec dfenv_1.12.0.zip' Content type 'application/zip' length 3307506 bytes opened URL downloaded 3229Kb package 'makecdfenv' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Documents and Settings\drnevich\Local Settings\Temp\RtmpCw5Rqb\downloaded_packages updating HTML package descriptions > library(makecdfenv) > cleancdfname(whatcdf("p0601_51.CEL")) Error in .Call("ReadHeader", filename, compress, PACKAGE = "affy") : C symbol name "ReadHeader" not in DLL for package "affy" I HOPE all the trouble I'm having below is related to this, and not to me! Because the 'whatcdf' isn't working, I tried to get the cdf name from an AffyBatch object: > raw <- ReadAffy() > raw at cdfName [1] "lund-zfa530237N" > cleancdfname(raw at cdfName) # the makecdf vignette says 'getCdfInfo' will look for an environment by this name for the AffyBatch [1] "lundzfa530237ncdf" > lundzfa530237ncdf <- make.cdf.env("lund-zfa530237N.cdf") Reading CDF file. Creating CDF environment Wait for about 231 dots.................................................................. .. ...................................................................... .. ...................................................................... .. ........... > length(ls(lundzfa530237ncdf)) #from the help file of 'make.cdf.env", so I think it's been created properly... [1] 23136 # ...but... > raw Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain lund-zfa530237N Library - package lundzfa530237ncdf not installed Data for package affy did not contain lundzfa530237ncdf Bioconductor - lundzfa530237ncdf not available AffyBatch object size of arrays=754x754 features (53306 kb) cdf=lund-zfa530237N (??? affyids) number of samples=12 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain lund-zfa530237N Library - package lundzfa530237ncdf not installed Data for package affy did not contain lundzfa530237ncdf Bioconductor - lundzfa530237ncdf not available In addition: Warning message: missing cdf environment ! in: show(<s4 object="" of="" class="" "affybatch"="">) I searched the archives and found this thread from Jim about the seemingly same error: >> I do not get any errors, but when I try to look at the affybatch object >> get the following message: >> >> Error in getCdfInfo(object) : Could not obtain CDF environment, problems >> encountered: >> specified environment does not contain XXX Library - package XXXcdf not >> installed Data for package affy did not contain XXXcdf Bioconductor - >> XXXcdf not available AffyBatch object size of arrays=291x291 features >> (15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in >> getCdfInfo(object) : Could not obtain CDF environment, problems >> encountered: >> Specified environment does not contain XXX > >This line is a hint, although rather oblique. When the affy package >looks for an environment in the current .GlobalEnv, it expects it to be >named XXX, so if you use make.cdf.env, you should name it XXX. OK, so this is contrary to what it says in the vignette, but I try it anyway: > rm(lundzfa530237ncdf) > lundzfa530237n <- make.cdf.env("lund-zfa530237N.cdf") Reading CDF file. Creating CDF environment Wait for about 231 dots.................................................................. .. ...................................................................... .. ...................................................................... .. ................................ But still no luck! > raw Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain lund-zfa530237N Library - package lundzfa530237ncdf not installed Data for package affy did not contain lundzfa530237ncdf Bioconductor - lundzfa530237ncdf not available AffyBatch object size of arrays=754x754 features (53306 kb) cdf=lund-zfa530237N (??? affyids) number of samples=12 Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain lund-zfa530237N Library - package lundzfa530237ncdf not installed Data for package affy did not contain lundzfa530237ncdf Bioconductor - lundzfa530237ncdf not available In addition: Warning message: missing cdf environment ! in: show(<s4 object="" of="" class="" "affybatch"="">) Am I doing anything wrong? I can't figure out what it could be for the life of me!!! Contents of workspace and sessionInfo below. Thanks, Jenny > ls() [1] "biocinstall" "biocinstall.affyPkgs" [3] "biocinstall.allPkgs" "biocinstall.defaultPkgs" [5] "biocinstall.graphPkgs" "biocinstall.litePkgs" [7] "biocinstall.monographPkgs" "biocLite" [9] "lundzfa530237n" "raw" > sessionInfo() R version 2.4.0 (2006-10-03) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] "splines" "tools" "methods" "stats" "graphics" "grDevices" [7] "utils" "datasets" "base" other attached packages: makecdfenv affyQCReport simpleaffy made4 scatterplot3d "1.12.0" "1.12.0" "2.8.0" "1.8.0" "0.3-24" ade4 affyPLM gcrma matchprobes affydata "1.4-2" "1.10.0" "2.6.0" "1.6.0" "1.10.0" affycoretools biomaRt RCurl XML GOstats "1.6.0" "1.8.0" "0.7-0" "0.99-93" "2.0.0" Category genefilter survival KEGG RBGL "2.0.0" "1.12.0" "2.29" "1.14.0" "1.10.0" annotate GO graph limma affy "1.12.0" "1.14.0" "1.12.0" "2.9.1" "1.12.0" affyio Biobase RWinEdt "1.2.0" "1.12.2" "1.7-5" > > > I do not get any errors, but when I try to look at the affybatch object > > I get the following message: > > > > Error in getCdfInfo(object) : Could not obtain CDF environment, problems > > encountered: > > Specified environment does not contain XXX Library - package XXXcdf not > > installed Data for package affy did not contain XXXcdf Bioconductor - > > XXXcdf not available AffyBatch object size of arrays=291x291 features > > (15887 kb) cdf=XXX (??? affyids) number of samples=24 Error in > > getCdfInfo(object) : Could not obtain CDF environment, problems > > encountered: > > Specified environment does not contain XXX > >This line is a hint, although rather oblique. When the affy package >looks for an environment in the current .GlobalEnv, it expects it to be >named XXX, so if you use make.cdf.env, you should name it XXX. However, >if it looks for a package, it has to be named xxxcdf. The best bet is to >allow make.cdf.package to do the package naming itself, because it will >be 100% correct. > > > > > I have tried putting the CDF file (created by BioC) in the R libraries > > folder with other libraries, but no luck. > >Nope. You have to install. This would have worked for maybe R-1.7.0 or >so, but modern versions of R require you to install the right way. > >HTH, > >Jim > > > > > In the makecdfenv vignette it says to "open a terminal with an operating > > system shell and write R CMD INSTALL XXXcdf", but I don't know how to do > > this on windows. > > > > Any suggestions would be greatly appreciated! > > > > Ann > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > -------------------------------------------------------- > > > > > > This email is confidential and intended solely for the use o...{{dropped}} > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > >-- >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. > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at uiuc.edu _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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