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Question: .cel file processing is not working for an old array
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gravatar for Maria Kesa
3.5 years ago by
Maria Kesa30
Maria Kesa30 wrote:
*Hello,* *I am trying to process very old .cel files from here: http://www.broadinstitute.org/cgi- bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75 <http: www.broadinstitute.org="" cgi-="" bin="" cancer="" publications="" pub_paper.cgi?mode="view&amp;paper_id=75">* *I have the newest version of R and updated BiocLite. * With the following code I get the error: library(affy) setwd("/home/maria/Documents/Work with Pietro/Prostate Cancer") for (i in 1:9) { obj_name<-paste('N0',i,'__normal.CEL',sep="") Data<-ReadAffy(filenames=obj_name) eset<-rma(Data) filename<-paste('sample',i,'.txt',sep="",collapse="") write.exprs(eset, file=filename, sep="\t") } trying URL ' http://bioconductor.org/packages/2.13/data/annotation/src/contrib/hgu9 5av2cdf_2.13.0.tar.gz ' Content type 'application/x-gzip' length 1341545 bytes (1.3 Mb) opened URL ================================================== downloaded 1.3 Mb * installing *source* package ‘hgu95av2cdf’ ... ** R ** data ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Error : .onLoad failed in loadNamespace() for 'hgu95av2cdf', details: call: NULL error: package ‘AnnotationDbi’ was built before R 3.0.0: please re-install it Error: loading failed Execution halted ERROR: loading failed * removing ‘/home/maria/R/x86_64-pc-linux-gnu- library/3.0/hgu95av2cdf’ The downloaded source packages are in ‘/tmp/RtmpRETXHh/downloaded_packages’ Show Traceback Rerun with Debug Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain HG_U95Av2 Library - package hgu95av2cdf not installed Library - package hgu95av2cdf not installed In addition: Warning message: In install.packages(cdfname, lib = lib, repos = biocinstallRepos(), : installation of package ‘hgu95av2cdf’ had non-zero exit status *When I try to install HG_U95Av2, I get the message:* biocLite("HG_U95Av2") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2. Installing package(s) 'HG_U95Av2' Old packages: 'AnnotationDbi' Update all/some/none? [a/s/n]: a trying URL ' http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi_1 .24.0.tar.gz ' Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) opened URL ================================================== downloaded 4.1 Mb * installing *source* package ‘AnnotationDbi’ ... ** R ** inst ** preparing package for lazy loading Error : package ‘DBI’ was built before R 3.0.0: please re-install it ERROR: lazy loading failed for package ‘AnnotationDbi’ * removing ‘/usr/local/lib/R/site-library/AnnotationDbi’ * restoring previous ‘/usr/local/lib/R/site-library/AnnotationDbi’ The downloaded source packages are in ‘/tmp/RtmpRETXHh/downloaded_packages’ Warning messages: 1: package ‘HG_U95Av2’ is not available (for R version 3.0.2) 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘AnnotationDbi’ had non-zero exit status *When I try to install 'AnnotationDbi' I get*. > biocLite("AnnotationDbi") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.1), R version 3.0.2. Installing package(s) 'AnnotationDbi' trying URL ' http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi_1 .24.0.tar.gz ' Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) opened URL ================================================== downloaded 4.1 Mb * installing *source* package ‘AnnotationDbi’ ... ** R ** inst ** preparing package for lazy loading Error : package ‘DBI’ was built before R 3.0.0: please re-install it ERROR: lazy loading failed for package ‘AnnotationDbi’ * removing ‘/home/maria/R/x86_64-pc-linux-gnu- library/3.0/AnnotationDbi’ The downloaded source packages are in ‘/tmp/RtmpRETXHh/downloaded_packages’ Old packages: 'AnnotationDbi' Update all/some/none? [a/s/n]: a trying URL ' http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi_1 .24.0.tar.gz ' Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) opened URL ================================================== downloaded 4.1 Mb * installing *source* package ‘AnnotationDbi’ ... ** R ** inst ** preparing package for lazy loading Error : package ‘DBI’ was built before R 3.0.0: please re-install it ERROR: lazy loading failed for package ‘AnnotationDbi’ * removing ‘/usr/local/lib/R/site-library/AnnotationDbi’ * restoring previous ‘/usr/local/lib/R/site-library/AnnotationDbi’ The downloaded source packages are in ‘/tmp/RtmpRETXHh/downloaded_packages’ Warning messages: 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package ‘AnnotationDbi’ had non-zero exit status 2: In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, : installation of package ‘AnnotationDbi’ had non-zero exit status > *I would really aporeciate the help! *Is there any chance that I can parse these old .cel files? Thank you, Maria Kesa [[alternative HTML version deleted]]
ADD COMMENTlink modified 3.5 years ago by James W. MacDonald45k • written 3.5 years ago by Maria Kesa30
0
gravatar for Sean Davis
3.5 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
Looks like your DBI package is broken. Try remove.packages("DBI") and try again. Sean On Jul 27, 2014 1:53 AM, "Maria Kesa" <maria.kesa@gmail.com> wrote: > *Hello,* > > > *I am trying to process very old .cel files from here: > > http://www.broadinstitute.org/cgi- bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75 > < > http://www.broadinstitute.org/cgi- bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75 > >* > > *I have the newest version of R and updated BiocLite. * > With the following code I get the error: > library(affy) > setwd("/home/maria/Documents/Work with Pietro/Prostate Cancer") > for (i in 1:9) { > obj_name<-paste('N0',i,'__normal.CEL',sep="") > Data<-ReadAffy(filenames=obj_name) > eset<-rma(Data) > filename<-paste('sample',i,'.txt',sep="",collapse="") > write.exprs(eset, file=filename, sep="\t") > } > > trying URL ' > > http://bioconductor.org/packages/2.13/data/annotation/src/contrib/hg u95av2cdf_2.13.0.tar.gz > ' > Content type 'application/x-gzip' length 1341545 bytes (1.3 Mb) > opened URL > ================================================== > downloaded 1.3 Mb > > * installing *source* package ‘hgu95av2cdf’ ... > ** R > ** data > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > Error : .onLoad failed in loadNamespace() for 'hgu95av2cdf', details: > call: NULL > error: package ‘AnnotationDbi’ was built before R 3.0.0: please > re-install it > Error: loading failed > Execution halted > ERROR: loading failed > * removing ‘/home/maria/R/x86_64-pc-linux-gnu- library/3.0/hgu95av2cdf’ > > The downloaded source packages are in > ‘/tmp/RtmpRETXHh/downloaded_packages’ > Show Traceback > > Rerun with Debug > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain HG_U95Av2 > Library - package hgu95av2cdf not installed > Library - package hgu95av2cdf not installed In addition: Warning message: > In install.packages(cdfname, lib = lib, repos = biocinstallRepos(), : > installation of package ‘hgu95av2cdf’ had non-zero exit status > > *When I try to install HG_U95Av2, I get the message:* > > biocLite("HG_U95Av2") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), > R version 3.0.2. > Installing package(s) 'HG_U95Av2' > Old packages: 'AnnotationDbi' > Update all/some/none? [a/s/n]: > a > trying URL ' > > http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi _1.24.0.tar.gz > ' > Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) > opened URL > ================================================== > downloaded 4.1 Mb > > * installing *source* package ‘AnnotationDbi’ ... > ** R > ** inst > ** preparing package for lazy loading > Error : package ‘DBI’ was built before R 3.0.0: please re- install it > ERROR: lazy loading failed for package ‘AnnotationDbi’ > * removing ‘/usr/local/lib/R/site-library/AnnotationDbi’ > * restoring previous ‘/usr/local/lib/R/site- library/AnnotationDbi’ > > The downloaded source packages are in > ‘/tmp/RtmpRETXHh/downloaded_packages’ > Warning messages: > 1: package ‘HG_U95Av2’ is not available (for R version 3.0.2) > 2: In install.packages(update[instlib == l, "Package"], l, contriburl = > contriburl, : > installation of package ‘AnnotationDbi’ had non-zero exit status > > *When I try to install 'AnnotationDbi' I get*. > > > biocLite("AnnotationDbi") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), > R version 3.0.2. > Installing package(s) 'AnnotationDbi' > trying URL ' > > http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi _1.24.0.tar.gz > ' > Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) > opened URL > ================================================== > downloaded 4.1 Mb > > * installing *source* package ‘AnnotationDbi’ ... > ** R > ** inst > ** preparing package for lazy loading > Error : package ‘DBI’ was built before R 3.0.0: please re- install it > ERROR: lazy loading failed for package ‘AnnotationDbi’ > * removing ‘/home/maria/R/x86_64-pc-linux-gnu- library/3.0/AnnotationDbi’ > > The downloaded source packages are in > ‘/tmp/RtmpRETXHh/downloaded_packages’ > Old packages: 'AnnotationDbi' > Update all/some/none? [a/s/n]: > a > trying URL ' > > http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi _1.24.0.tar.gz > ' > Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) > opened URL > ================================================== > downloaded 4.1 Mb > > * installing *source* package ‘AnnotationDbi’ ... > ** R > ** inst > ** preparing package for lazy loading > Error : package ‘DBI’ was built before R 3.0.0: please re- install it > ERROR: lazy loading failed for package ‘AnnotationDbi’ > * removing ‘/usr/local/lib/R/site-library/AnnotationDbi’ > * restoring previous ‘/usr/local/lib/R/site- library/AnnotationDbi’ > > The downloaded source packages are in > ‘/tmp/RtmpRETXHh/downloaded_packages’ > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ‘AnnotationDbi’ had non-zero exit status > 2: In install.packages(update[instlib == l, "Package"], l, contriburl = > contriburl, : > installation of package ‘AnnotationDbi’ had non-zero exit status > > > *I would really aporeciate the help! *Is there any chance that I can parse > these old .cel files? > > Thank you, > Maria Kesa > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 3.5 years ago by Sean Davis21k
Thank you, but I still get the same error message! My friend's computer has no problem with my script. There seems to be a problem with ‘hgu95av2cdf’ library. Further advice would be greatly aporeciated! Maria On Sun, Jul 27, 2014 at 1:58 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > Looks like your DBI package is broken. Try remove.packages("DBI") and try > again. > > Sean > On Jul 27, 2014 1:53 AM, "Maria Kesa" <maria.kesa@gmail.com> wrote: > >> *Hello,* >> >> >> *I am trying to process very old .cel files from here: >> >> http://www.broadinstitute.org/cgi- bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75 >> < >> http://www.broadinstitute.org/cgi- bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75 >> >* >> >> *I have the newest version of R and updated BiocLite. * >> >> With the following code I get the error: >> library(affy) >> setwd("/home/maria/Documents/Work with Pietro/Prostate Cancer") >> for (i in 1:9) { >> obj_name<-paste('N0',i,'__normal.CEL',sep="") >> Data<-ReadAffy(filenames=obj_name) >> eset<-rma(Data) >> filename<-paste('sample',i,'.txt',sep="",collapse="") >> write.exprs(eset, file=filename, sep="\t") >> } >> >> trying URL ' >> >> http://bioconductor.org/packages/2.13/data/annotation/src/contrib/h gu95av2cdf_2.13.0.tar.gz >> ' >> Content type 'application/x-gzip' length 1341545 bytes (1.3 Mb) >> opened URL >> ================================================== >> downloaded 1.3 Mb >> >> * installing *source* package ‘hgu95av2cdf’ ... >> ** R >> ** data >> ** preparing package for lazy loading >> ** help >> *** installing help indices >> ** building package indices >> ** testing if installed package can be loaded >> Error : .onLoad failed in loadNamespace() for 'hgu95av2cdf', details: >> call: NULL >> error: package ‘AnnotationDbi’ was built before R 3.0.0: please >> re-install it >> Error: loading failed >> Execution halted >> ERROR: loading failed >> * removing ‘/home/maria/R/x86_64-pc-linux-gnu- library/3.0/hgu95av2cdf’ >> >> The downloaded source packages are in >> ‘/tmp/RtmpRETXHh/downloaded_packages’ >> Show Traceback >> >> Rerun with Debug >> Error in getCdfInfo(object) : >> Could not obtain CDF environment, problems encountered: >> Specified environment does not contain HG_U95Av2 >> Library - package hgu95av2cdf not installed >> Library - package hgu95av2cdf not installed In addition: Warning message: >> In install.packages(cdfname, lib = lib, repos = biocinstallRepos(), : >> installation of package ‘hgu95av2cdf’ had non-zero exit status >> >> *When I try to install HG_U95Av2, I get the message:* >> >> >> biocLite("HG_U95Av2") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), >> R version 3.0.2. >> Installing package(s) 'HG_U95Av2' >> Old packages: 'AnnotationDbi' >> Update all/some/none? [a/s/n]: >> a >> trying URL ' >> >> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDb i_1.24.0.tar.gz >> ' >> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) >> opened URL >> ================================================== >> downloaded 4.1 Mb >> >> * installing *source* package ‘AnnotationDbi’ ... >> ** R >> ** inst >> ** preparing package for lazy loading >> Error : package ‘DBI’ was built before R 3.0.0: please re- install it >> ERROR: lazy loading failed for package ‘AnnotationDbi’ >> * removing ‘/usr/local/lib/R/site-library/AnnotationDbi’ >> * restoring previous ‘/usr/local/lib/R/site- library/AnnotationDbi’ >> >> The downloaded source packages are in >> ‘/tmp/RtmpRETXHh/downloaded_packages’ >> Warning messages: >> 1: package ‘HG_U95Av2’ is not available (for R version 3.0.2) >> 2: In install.packages(update[instlib == l, "Package"], l, contriburl = >> contriburl, : >> installation of package ‘AnnotationDbi’ had non-zero exit status >> >> *When I try to install 'AnnotationDbi' I get*. >> >> >> > biocLite("AnnotationDbi") >> BioC_mirror: http://bioconductor.org >> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), >> R version 3.0.2. >> Installing package(s) 'AnnotationDbi' >> trying URL ' >> >> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDb i_1.24.0.tar.gz >> ' >> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) >> opened URL >> ================================================== >> downloaded 4.1 Mb >> >> * installing *source* package ‘AnnotationDbi’ ... >> ** R >> ** inst >> ** preparing package for lazy loading >> Error : package ‘DBI’ was built before R 3.0.0: please re- install it >> ERROR: lazy loading failed for package ‘AnnotationDbi’ >> * removing ‘/home/maria/R/x86_64-pc-linux-gnu- library/3.0/AnnotationDbi’ >> >> The downloaded source packages are in >> ‘/tmp/RtmpRETXHh/downloaded_packages’ >> Old packages: 'AnnotationDbi' >> Update all/some/none? [a/s/n]: >> a >> trying URL ' >> >> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDb i_1.24.0.tar.gz >> ' >> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) >> opened URL >> ================================================== >> downloaded 4.1 Mb >> >> * installing *source* package ‘AnnotationDbi’ ... >> ** R >> ** inst >> ** preparing package for lazy loading >> Error : package ‘DBI’ was built before R 3.0.0: please re- install it >> ERROR: lazy loading failed for package ‘AnnotationDbi’ >> * removing ‘/usr/local/lib/R/site-library/AnnotationDbi’ >> * restoring previous ‘/usr/local/lib/R/site- library/AnnotationDbi’ >> >> The downloaded source packages are in >> ‘/tmp/RtmpRETXHh/downloaded_packages’ >> Warning messages: >> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >> installation of package ‘AnnotationDbi’ had non-zero exit status >> 2: In install.packages(update[instlib == l, "Package"], l, contriburl = >> contriburl, : >> installation of package ‘AnnotationDbi’ had non-zero exit status >> > >> *I would really aporeciate the help! *Is there any chance that I can parse >> >> these old .cel files? >> >> Thank you, >> Maria Kesa >> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > [[alternative HTML version deleted]]
ADD REPLYlink written 3.5 years ago by Maria Kesa30
On 07/27/2014 01:20 PM, Maria Kesa wrote: > Thank you, but I still get the same error message! My friend's computer has > no problem with my script. There seems to be a problem with > > ???hgu95av2cdf??? library. Further advice would be greatly aporeciated! > > > Maria > > > > On Sun, Jul 27, 2014 at 1:58 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: > >> Looks like your DBI package is broken. Try remove.packages("DBI") and try >> again. >> >> Sean >> On Jul 27, 2014 1:53 AM, "Maria Kesa" <maria.kesa at="" gmail.com=""> wrote: >> >>> *Hello,* >>> >>> >>> *I am trying to process very old .cel files from here: >>> >>> http://www.broadinstitute.org/cgi- bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75 >>> < >>> http://www.broadinstitute.org/cgi- bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75 >>>> * >>> >>> *I have the newest version of R and updated BiocLite. * >>> >>> With the following code I get the error: >>> library(affy) >>> setwd("/home/maria/Documents/Work with Pietro/Prostate Cancer") >>> for (i in 1:9) { >>> obj_name<-paste('N0',i,'__normal.CEL',sep="") >>> Data<-ReadAffy(filenames=obj_name) >>> eset<-rma(Data) >>> filename<-paste('sample',i,'.txt',sep="",collapse="") >>> write.exprs(eset, file=filename, sep="\t") >>> } >>> >>> trying URL ' >>> >>> http://bioconductor.org/packages/2.13/data/annotation/src/contrib/ hgu95av2cdf_2.13.0.tar.gz >>> ' >>> Content type 'application/x-gzip' length 1341545 bytes (1.3 Mb) >>> opened URL >>> ================================================== >>> downloaded 1.3 Mb >>> >>> * installing *source* package ???hgu95av2cdf??? ... >>> ** R >>> ** data >>> ** preparing package for lazy loading >>> ** help >>> *** installing help indices >>> ** building package indices >>> ** testing if installed package can be loaded >>> Error : .onLoad failed in loadNamespace() for 'hgu95av2cdf', details: >>> call: NULL >>> error: package ???AnnotationDbi??? was built before R 3.0.0: please this says that the AnnotationDbi package is out of date. try biocLite() and respond 'y' when asked if you'd like to update out-of-date packages. If you continue to have problems, then post the entire session where the biocLite() command is executed. Martin >>> re-install it >>> Error: loading failed >>> Execution halted >>> ERROR: loading failed >>> * removing ???/home/maria/R/x86_64-pc-linux-gnu- library/3.0/hgu95av2cdf??? >>> >>> The downloaded source packages are in >>> ???/tmp/RtmpRETXHh/downloaded_packages??? >>> Show Traceback >>> >>> Rerun with Debug >>> Error in getCdfInfo(object) : >>> Could not obtain CDF environment, problems encountered: >>> Specified environment does not contain HG_U95Av2 >>> Library - package hgu95av2cdf not installed >>> Library - package hgu95av2cdf not installed In addition: Warning message: >>> In install.packages(cdfname, lib = lib, repos = biocinstallRepos(), : >>> installation of package ???hgu95av2cdf??? had non-zero exit status >>> >>> *When I try to install HG_U95Av2, I get the message:* >>> >>> >>> biocLite("HG_U95Av2") >>> BioC_mirror: http://bioconductor.org >>> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), >>> R version 3.0.2. >>> Installing package(s) 'HG_U95Av2' >>> Old packages: 'AnnotationDbi' >>> Update all/some/none? [a/s/n]: >>> a >>> trying URL ' >>> >>> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationD bi_1.24.0.tar.gz >>> ' >>> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) >>> opened URL >>> ================================================== >>> downloaded 4.1 Mb >>> >>> * installing *source* package ???AnnotationDbi??? ... >>> ** R >>> ** inst >>> ** preparing package for lazy loading >>> Error : package ???DBI??? was built before R 3.0.0: please re- install it >>> ERROR: lazy loading failed for package ???AnnotationDbi??? >>> * removing ???/usr/local/lib/R/site-library/AnnotationDbi??? >>> * restoring previous ???/usr/local/lib/R/site- library/AnnotationDbi??? >>> >>> The downloaded source packages are in >>> ???/tmp/RtmpRETXHh/downloaded_packages??? >>> Warning messages: >>> 1: package ???HG_U95Av2??? is not available (for R version 3.0.2) >>> 2: In install.packages(update[instlib == l, "Package"], l, contriburl = >>> contriburl, : >>> installation of package ???AnnotationDbi??? had non-zero exit status >>> >>> *When I try to install 'AnnotationDbi' I get*. >>> >>> >>>> biocLite("AnnotationDbi") >>> BioC_mirror: http://bioconductor.org >>> Using Bioconductor version 2.13 (BiocInstaller 1.12.1), >>> R version 3.0.2. >>> Installing package(s) 'AnnotationDbi' >>> trying URL ' >>> >>> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationD bi_1.24.0.tar.gz >>> ' >>> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) >>> opened URL >>> ================================================== >>> downloaded 4.1 Mb >>> >>> * installing *source* package ???AnnotationDbi??? ... >>> ** R >>> ** inst >>> ** preparing package for lazy loading >>> Error : package ???DBI??? was built before R 3.0.0: please re- install it >>> ERROR: lazy loading failed for package ???AnnotationDbi??? >>> * removing ???/home/maria/R/x86_64-pc-linux-gnu- library/3.0/AnnotationDbi??? >>> >>> The downloaded source packages are in >>> ???/tmp/RtmpRETXHh/downloaded_packages??? >>> Old packages: 'AnnotationDbi' >>> Update all/some/none? [a/s/n]: >>> a >>> trying URL ' >>> >>> http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationD bi_1.24.0.tar.gz >>> ' >>> Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) >>> opened URL >>> ================================================== >>> downloaded 4.1 Mb >>> >>> * installing *source* package ???AnnotationDbi??? ... >>> ** R >>> ** inst >>> ** preparing package for lazy loading >>> Error : package ???DBI??? was built before R 3.0.0: please re- install it >>> ERROR: lazy loading failed for package ???AnnotationDbi??? >>> * removing ???/usr/local/lib/R/site-library/AnnotationDbi??? >>> * restoring previous ???/usr/local/lib/R/site- library/AnnotationDbi??? >>> >>> The downloaded source packages are in >>> ???/tmp/RtmpRETXHh/downloaded_packages??? >>> Warning messages: >>> 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : >>> installation of package ???AnnotationDbi??? had non-zero exit status >>> 2: In install.packages(update[instlib == l, "Package"], l, contriburl = >>> contriburl, : >>> installation of package ???AnnotationDbi??? had non-zero exit status >>>> >>> *I would really aporeciate the help! *Is there any chance that I can parse >>> >>> these old .cel files? >>> >>> Thank you, >>> Maria Kesa >>> >>> [[alternative HTML version deleted]] >>> >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
ADD REPLYlink written 3.5 years ago by Martin Morgan ♦♦ 21k
0
gravatar for James W. MacDonald
3.5 years ago by
United States
James W. MacDonald45k wrote:
Hi Maria, Sean and Martin have already given you feedback about updating your AnnotationDbi package, so I won't comment further on that issue. But I will note that the for() loop you are using below is almost surely not what you want to be doing. The RMA algorithm uses information from all arrays in an experiment to help generate expression values. By running rma() individually on each array, you are eliminating that (very important) aspect of the algorithm. The conventional thing to do is setwd("/home/maria/Documents/Work with Pietro/Prostate Cancer") Data<-ReadAffy() eset <- rma(Data) and then the ExpressionSet will contain normalized data for all nine arrays. But this makes an assumption that these arrays are all from the same experiment, so a quantile normalization makes sense. If they are not all from the same experiment, or you have other reasons to suspect that a quantile normalization for all arrays is not sensible, you should instead be using the frma package, which is designed to allow you to process samples singly using the RMA algorithm. Best, Jim On 7/26/2014 6:38 PM, Maria Kesa wrote: > *Hello,* > > > *I am trying to process very old .cel files from here: > http://www.broadinstitute.org/cgi- bin/cancer/publications/pub_paper.cgi?mode=view&paper_id=75 > <http: www.broadinstitute.org="" cgi-="" bin="" cancer="" publications="" pub_paper.cgi?mode="view&amp;paper_id=75">* > > *I have the newest version of R and updated BiocLite. * > With the following code I get the error: > library(affy) > setwd("/home/maria/Documents/Work with Pietro/Prostate Cancer") > for (i in 1:9) { > obj_name<-paste('N0',i,'__normal.CEL',sep="") > Data<-ReadAffy(filenames=obj_name) > eset<-rma(Data) > filename<-paste('sample',i,'.txt',sep="",collapse="") > write.exprs(eset, file=filename, sep="\t") > } > > trying URL ' > http://bioconductor.org/packages/2.13/data/annotation/src/contrib/hg u95av2cdf_2.13.0.tar.gz > ' > Content type 'application/x-gzip' length 1341545 bytes (1.3 Mb) > opened URL > ================================================== > downloaded 1.3 Mb > > * installing *source* package ???hgu95av2cdf??? ... > ** R > ** data > ** preparing package for lazy loading > ** help > *** installing help indices > ** building package indices > ** testing if installed package can be loaded > Error : .onLoad failed in loadNamespace() for 'hgu95av2cdf', details: > call: NULL > error: package ???AnnotationDbi??? was built before R 3.0.0: please > re-install it > Error: loading failed > Execution halted > ERROR: loading failed > * removing ???/home/maria/R/x86_64-pc-linux-gnu- library/3.0/hgu95av2cdf??? > > The downloaded source packages are in > ???/tmp/RtmpRETXHh/downloaded_packages??? > Show Traceback > > Rerun with Debug > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain HG_U95Av2 > Library - package hgu95av2cdf not installed > Library - package hgu95av2cdf not installed In addition: Warning message: > In install.packages(cdfname, lib = lib, repos = biocinstallRepos(), : > installation of package ???hgu95av2cdf??? had non-zero exit status > > *When I try to install HG_U95Av2, I get the message:* > > biocLite("HG_U95Av2") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), > R version 3.0.2. > Installing package(s) 'HG_U95Av2' > Old packages: 'AnnotationDbi' > Update all/some/none? [a/s/n]: > a > trying URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi _1.24.0.tar.gz > ' > Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) > opened URL > ================================================== > downloaded 4.1 Mb > > * installing *source* package ???AnnotationDbi??? ... > ** R > ** inst > ** preparing package for lazy loading > Error : package ???DBI??? was built before R 3.0.0: please re- install it > ERROR: lazy loading failed for package ???AnnotationDbi??? > * removing ???/usr/local/lib/R/site-library/AnnotationDbi??? > * restoring previous ???/usr/local/lib/R/site- library/AnnotationDbi??? > > The downloaded source packages are in > ???/tmp/RtmpRETXHh/downloaded_packages??? > Warning messages: > 1: package ???HG_U95Av2??? is not available (for R version 3.0.2) > 2: In install.packages(update[instlib == l, "Package"], l, contriburl = > contriburl, : > installation of package ???AnnotationDbi??? had non-zero exit status > > *When I try to install 'AnnotationDbi' I get*. > >> biocLite("AnnotationDbi") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.1), > R version 3.0.2. > Installing package(s) 'AnnotationDbi' > trying URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi _1.24.0.tar.gz > ' > Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) > opened URL > ================================================== > downloaded 4.1 Mb > > * installing *source* package ???AnnotationDbi??? ... > ** R > ** inst > ** preparing package for lazy loading > Error : package ???DBI??? was built before R 3.0.0: please re- install it > ERROR: lazy loading failed for package ???AnnotationDbi??? > * removing ???/home/maria/R/x86_64-pc-linux-gnu- library/3.0/AnnotationDbi??? > > The downloaded source packages are in > ???/tmp/RtmpRETXHh/downloaded_packages??? > Old packages: 'AnnotationDbi' > Update all/some/none? [a/s/n]: > a > trying URL ' > http://bioconductor.org/packages/2.13/bioc/src/contrib/AnnotationDbi _1.24.0.tar.gz > ' > Content type 'application/x-gzip' length 4317449 bytes (4.1 Mb) > opened URL > ================================================== > downloaded 4.1 Mb > > * installing *source* package ???AnnotationDbi??? ... > ** R > ** inst > ** preparing package for lazy loading > Error : package ???DBI??? was built before R 3.0.0: please re- install it > ERROR: lazy loading failed for package ???AnnotationDbi??? > * removing ???/usr/local/lib/R/site-library/AnnotationDbi??? > * restoring previous ???/usr/local/lib/R/site- library/AnnotationDbi??? > > The downloaded source packages are in > ???/tmp/RtmpRETXHh/downloaded_packages??? > Warning messages: > 1: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package ???AnnotationDbi??? had non-zero exit status > 2: In install.packages(update[instlib == l, "Package"], l, contriburl = > contriburl, : > installation of package ???AnnotationDbi??? had non-zero exit status >> > *I would really aporeciate the help! *Is there any chance that I can parse > these old .cel files? > > Thank you, > Maria Kesa > > [[alternative HTML version deleted]] > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > 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 University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 3.5 years ago by James W. MacDonald45k
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