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