Question: ReadAffy - Error VECTOR_ELT() can only be applied to a 'list', not a 'char'
0
gravatar for Aedin Culhane
12.5 years ago by
Aedin Culhane510
United States
Aedin Culhane510 wrote:
Hi BioC, I am having problems getting ReadAffy to work on fc5. Any ideas? Thanks. Aedin > example(ReadAffy) RdAffy> if(require(affydata)){ RdAffy+ celpath <- system.file("celfiles", package="affydata") RdAffy+ fns <- list.celfiles(path=celpath,full.names=TRUE) RdAffy+ RdAffy+ cat("Reading files:\n",paste(fns,collapse="\n"),"\n") RdAffy+ ##read a binary celfile RdAffy+ abatch <- ReadAffy(filenames=fns[1]) RdAffy+ ##read a text celfile RdAffy+ abatch <- ReadAffy(filenames=fns[2]) RdAffy+ ##read all files in that dir RdAffy+ abatch <- ReadAffy(celfile.path=celpath) RdAffy+ } Loading required package: affydata Reading files: /home/aedin/R/i686-redhat-linux-gnu- library/2.5/affydata/celfiles/binary.cel /home/aedin/R/i686-redhat-linux-gnu- library/2.5/affydata/celfiles/text.cel Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : VECTOR_ELT() can only be applied to a 'list', not a 'char' > sessionInfo() R version 2.5.0 (2007-04-23) i686-redhat-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_MESSAGE S=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_IDENTIFI CATION=C attached base packages: [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" [7] "methods" "base" other attached packages: affydata affy affyio Biobase "1.11.2" "1.14.1" "1.0.0" "1.14.0"
affy affyio • 1.9k views
ADD COMMENTlink modified 12.5 years ago by Ben Bolstad1.2k • written 12.5 years ago by Aedin Culhane510
Answer: ReadAffy - Error VECTOR_ELT() can only be applied to a 'list', not a 'char'
0
gravatar for Ben Bolstad
12.5 years ago by
Ben Bolstad1.2k
Ben Bolstad1.2k wrote:
You have a mismatch between your version of affy and your version of affyio. You need 1.4.0 or later (the version released with BioC2.0). As a general rule people should not be mixing and matching packages between different versions of BioC/R. It is always safest to re- install the release using biocLite() or getBioC() rather than trying to install packages manually and hoping it works. Best, Ben On Wed, 2007-06-20 at 19:38 -0400, aedin culhane wrote: > Hi BioC, > I am having problems getting ReadAffy to work on fc5. Any ideas? > Thanks. > Aedin > > > example(ReadAffy) > > RdAffy> if(require(affydata)){ > RdAffy+ celpath <- system.file("celfiles", package="affydata") > RdAffy+ fns <- list.celfiles(path=celpath,full.names=TRUE) > RdAffy+ > RdAffy+ cat("Reading files:\n",paste(fns,collapse="\n"),"\n") > RdAffy+ ##read a binary celfile > RdAffy+ abatch <- ReadAffy(filenames=fns[1]) > RdAffy+ ##read a text celfile > RdAffy+ abatch <- ReadAffy(filenames=fns[2]) > RdAffy+ ##read all files in that dir > RdAffy+ abatch <- ReadAffy(celfile.path=celpath) > RdAffy+ } > Loading required package: affydata > Reading files: > > /home/aedin/R/i686-redhat-linux-gnu- library/2.5/affydata/celfiles/binary.cel > /home/aedin/R/i686-redhat-linux-gnu- library/2.5/affydata/celfiles/text.cel > Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : > VECTOR_ELT() can only be applied to a 'list', not a 'char' > > > > > sessionInfo() > R version 2.5.0 (2007-04-23) > i686-redhat-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_MESSAGE > > S=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHO NE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFI > CATION=C > > attached base packages: > [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" > [7] "methods" "base" > > other attached packages: > affydata affy affyio Biobase > "1.11.2" "1.14.1" "1.0.0" "1.14.0" > > _______________________________________________ > 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
ADD COMMENTlink written 12.5 years ago by Ben Bolstad1.2k
Thanks Ben I did use biocLite() to do the update, so this is surprising. affyiio should have been installed as a dependency of affy. I used: source("http://www.bioconductor.org/biocLite.R") biocLite() I just installed affyio manually and now it works fine. Thanks for your help Aedin Ben Bolstad wrote: > You have a mismatch between your version of affy and your version of > affyio. You need 1.4.0 or later (the version released with BioC2.0). > > As a general rule people should not be mixing and matching packages > between different versions of BioC/R. It is always safest to re- install > the release using biocLite() or getBioC() rather than trying to install > packages manually and hoping it works. > > Best, > > Ben > > > > > > > On Wed, 2007-06-20 at 19:38 -0400, aedin culhane wrote: > >> Hi BioC, >> I am having problems getting ReadAffy to work on fc5. Any ideas? >> Thanks. >> Aedin >> >> > example(ReadAffy) >> >> RdAffy> if(require(affydata)){ >> RdAffy+ celpath <- system.file("celfiles", package="affydata") >> RdAffy+ fns <- list.celfiles(path=celpath,full.names=TRUE) >> RdAffy+ >> RdAffy+ cat("Reading files:\n",paste(fns,collapse="\n"),"\n") >> RdAffy+ ##read a binary celfile >> RdAffy+ abatch <- ReadAffy(filenames=fns[1]) >> RdAffy+ ##read a text celfile >> RdAffy+ abatch <- ReadAffy(filenames=fns[2]) >> RdAffy+ ##read all files in that dir >> RdAffy+ abatch <- ReadAffy(celfile.path=celpath) >> RdAffy+ } >> Loading required package: affydata >> Reading files: >> >> /home/aedin/R/i686-redhat-linux-gnu- library/2.5/affydata/celfiles/binary.cel >> /home/aedin/R/i686-redhat-linux-gnu- library/2.5/affydata/celfiles/text.cel >> Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData, : >> VECTOR_ELT() can only be applied to a 'list', not a 'char' >> >> >> >> > sessionInfo() >> R version 2.5.0 (2007-04-23) >> i686-redhat-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_MESSAGE >> >> S=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPH ONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFI >> CATION=C >> >> attached base packages: >> [1] "tools" "stats" "graphics" "grDevices" "utils" "datasets" >> [7] "methods" "base" >> >> other attached packages: >> affydata affy affyio Biobase >> "1.11.2" "1.14.1" "1.0.0" "1.14.0" >> >> _______________________________________________ >> 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 >> -- Aed?n Culhane Research Associate in Prof. J Quackenbush Lab Harvard School of Public Health, Dana-Farber Cancer Institute 44 Binney Street, SM822 Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute Boston, MA 02115 USA Phone: +1 (617) 632 2468 Fax: +1 (617) 582 7760 Email: aedin at jimmy.harvard.edu Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html
ADD REPLYlink written 12.5 years ago by Aedin Culhane510
you might also find the following useful: http://article.gmane.org/gmane.science.biology.informatics.conductor/ 12709/ b On Jun 20, 2007, at 10:54 PM, Aedin Culhane wrote: > Thanks Ben > I did use biocLite() to do the update, so this is surprising. affyiio > should have been installed as a dependency of affy. I used: > > source("http://www.bioconductor.org/biocLite.R") > biocLite() > > I just installed affyio manually and now it works fine. > > Thanks for your help > Aedin > > > Ben Bolstad wrote: >> You have a mismatch between your version of affy and your version of >> affyio. You need 1.4.0 or later (the version released with BioC2.0). >> >> As a general rule people should not be mixing and matching packages >> between different versions of BioC/R. It is always safest to re- >> install >> the release using biocLite() or getBioC() rather than trying to >> install >> packages manually and hoping it works. >> >> Best, >> >> Ben >> >> >> >> >> >> >> On Wed, 2007-06-20 at 19:38 -0400, aedin culhane wrote: >> >>> Hi BioC, >>> I am having problems getting ReadAffy to work on fc5. Any ideas? >>> Thanks. >>> Aedin >>> >>>> example(ReadAffy) >>> >>> RdAffy> if(require(affydata)){ >>> RdAffy+ celpath <- system.file("celfiles", package="affydata") >>> RdAffy+ fns <- list.celfiles(path=celpath,full.names=TRUE) >>> RdAffy+ >>> RdAffy+ cat("Reading files:\n",paste(fns,collapse="\n"),"\n") >>> RdAffy+ ##read a binary celfile >>> RdAffy+ abatch <- ReadAffy(filenames=fns[1]) >>> RdAffy+ ##read a text celfile >>> RdAffy+ abatch <- ReadAffy(filenames=fns[2]) >>> RdAffy+ ##read all files in that dir >>> RdAffy+ abatch <- ReadAffy(celfile.path=celpath) >>> RdAffy+ } >>> Loading required package: affydata >>> Reading files: >>> >>> /home/aedin/R/i686-redhat-linux-gnu-library/2.5/affydata/celfiles/ >>> binary.cel >>> /home/aedin/R/i686-redhat-linux-gnu-library/2.5/affydata/celfiles/ >>> text.cel >>> Error in read.affybatch(filenames = l$filenames, phenoData = l >>> $phenoData, : >>> VECTOR_ELT() can only be applied to a 'list', not a 'char' >>> >>> >>> >>>> sessionInfo() >>> R version 2.5.0 (2007-04-23) >>> i686-redhat-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_MESSAGE >>> >>> S=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHO >>> NE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFI >>> CATION=C >>> >>> attached base packages: >>> [1] "tools" "stats" "graphics" "grDevices" "utils" >>> "datasets" >>> [7] "methods" "base" >>> >>> other attached packages: >>> affydata affy affyio Biobase >>> "1.11.2" "1.14.1" "1.0.0" "1.14.0" >>> >>> _______________________________________________ >>> 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 >>> > > > -- > Aed?n Culhane > Research Associate in Prof. J Quackenbush Lab > Harvard School of Public Health, Dana-Farber Cancer Institute > > 44 Binney Street, SM822 > Department of Biostatistics and Computational Biology, > Dana-Farber Cancer Institute > Boston, MA 02115 > USA > > Phone: +1 (617) 632 2468 > Fax: +1 (617) 582 7760 > Email: aedin at jimmy.harvard.edu > Web URL: http://www.hsph.harvard.edu/researchers/aculhane.html > > _______________________________________________ > 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
ADD REPLYlink written 12.5 years ago by Benilton Carvalho4.3k
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