BiocLite eror
3
0
Entering edit mode
@rabia-johnson-6481
Last seen 8.1 years ago
HI, Object : problem with hgu133plus2.db you need to install this package to complete this step If possible can anyone help. I am new to R and are working through the tutorial of Daniel Swan (Analysing microarray data in BioConductor) Upon writing the following command I get the following error: > biocLite("hgu133plus2.db") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.3. Installing package(s) 'hgu133plus2.db' Warning: package 'hgu133plus2.db' is in use and will not be installed Warning message: installed directory not writable, cannot update packages 'boot', 'class', 'cluster', 'foreign', 'KernSmooth', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'rpart', 'spatial' Thus, needless to say when I continue with the next command I get more errors: > library(hgu133plus2.db) > library(annotate) > gene.symbols <- getSYMBOL(probeset.list$ID, "hgu133plus2") Error in unlist(lookUp(x, data, "SYMBOL")) : error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in lookUp(x, data, "SYMBOL") : No keys provided Can anyone help please Regards Rabia _______________________________________ Rabia Johnson (PhD) Senior Scientist South African Medical Research Council Diabetes Discovery Platform Building E Francie van Zijl Drive, Parow Valley, 7505, Cape Town Cell: +27 82 0677296 Tel: +27 21 938 0866 Fax: +27 21 938 0456 E-mail: rabia.johnson@mrc.ac.za Disclaimer\ \ The information contained in this communic...{{dropped:20}} Microarray hgu133plus2 Microarray hgu133plus2 • 1.8k views ADD COMMENT 0 Entering edit mode @steve-lianoglou-2771 Last seen 4 weeks ago United States Hi, On Wed, Apr 2, 2014 at 12:04 AM, Rabia Johnson <rabia.johnson at="" mrc.ac.za=""> wrote: > HI, > > Object : problem with hgu133plus2.db you need to install this package to complete this step > > If possible can anyone help. I am new to R and are working through the tutorial of Daniel Swan (Analysing microarray data in BioConductor) > Upon writing the following command I get the following error: > >> biocLite("hgu133plus2.db") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version 3.0.3. > Installing package(s) 'hgu133plus2.db' > Warning: package 'hgu133plus2.db' is in use and will not be installed > Warning message: > installed directory not writable, cannot update packages 'boot', 'class', > 'cluster', 'foreign', 'KernSmooth', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', > 'rpart', 'spatial' > > > Thus, needless to say when I continue with the next command I get more errors: > >> library(hgu133plus2.db) >> library(annotate) >> gene.symbols <- getSYMBOL(probeset.list$ID, "hgu133plus2") > Error in unlist(lookUp(x, data, "SYMBOL")) : > error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in lookUp(x, data, "SYMBOL") : No keys provided Perhaps your probeset.list$ID isn't what you think it is? What is the output of head(probeset.list$ID) ? -steve -- Steve Lianoglou Computational Biologist Genentech
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Entering edit mode
Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 19 months ago
United States
----- Original Message ----- > From: "Rabia Johnson" <rabia.johnson at="" mrc.ac.za=""> > To: bioconductor at r-project.org > Sent: Wednesday, April 2, 2014 12:04:19 AM > Subject: [BioC] BiocLite eror > > HI, > > Object : problem with hgu133plus2.db you need to install this > package to complete this step > > If possible can anyone help. I am new to R and are working through > the tutorial of Daniel Swan (Analysing microarray data in > BioConductor) > Upon writing the following command I get the following error: > > > biocLite("hgu133plus2.db") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version > 3.0.3. > Installing package(s) 'hgu133plus2.db' > Warning: package 'hgu133plus2.db' is in use and will not be installed > Warning message: > installed directory not writable, cannot update packages 'boot', > 'class', > 'cluster', 'foreign', 'KernSmooth', 'MASS', 'Matrix', 'mgcv', > 'nlme', 'nnet', > 'rpart', 'spatial' > > Try quitting your R session and starting a fresh one like this: R --vanilla And then running source("http://bioconductor.org/biocLite.R") biocLite("hgu133plus2.db") Does that work? Dan > Thus, needless to say when I continue with the next command I get > more errors: > > > library(hgu133plus2.db) > > library(annotate) > > gene.symbols <- getSYMBOL(probeset.list$ID, "hgu133plus2") > Error in unlist(lookUp(x, data, "SYMBOL")) : > error in evaluating the argument 'x' in selecting a method for > function 'unlist': Error in lookUp(x, data, "SYMBOL") : No keys > provided > > > Can anyone help please > Regards > Rabia > > > _______________________________________ > Rabia Johnson (PhD) > Senior Scientist > South African Medical Research Council > Diabetes Discovery Platform > Building E > Francie van Zijl Drive, Parow Valley, 7505, Cape Town > Cell: +27 82 0677296 > Tel: +27 21 938 0866 > Fax: +27 21 938 0456 > E-mail: rabia.johnson at mrc.ac.za > > > Disclaimer\ \ The information contained in this > communic...{{dropped:20}} > > _______________________________________________ > 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 > ADD COMMENT 0 Entering edit mode Dan Tenenbaum ★ 8.2k @dan-tenenbaum-4256 Last seen 19 months ago United States Please keep the bioconductor list added (use Reply All) so that all can learn and contribute. Please shut down ALL R sessions and then start a new one with R --vanilla. That should stop the R session that is "using" hgu133plus2.db. Dan ----- Original Message ----- > From: "Rabia Johnson" <rabia.johnson at="" mrc.ac.za=""> > To: "Dan Tenenbaum" <dtenenba at="" fhcrc.org=""> > Sent: Thursday, April 3, 2014 12:07:03 AM > Subject: RE: [BioC] BiocLite eror > > Dear Dan, > No unfortunately it does not. This is the error that I am getting: > > > > source("http://bioconductor.org/biocLite.R") > Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help > > biocLite("hgu133plus2.db") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version > 3.0.3. > Installing package(s) 'hgu133plus2.db' > Warning: package ?hgu133plus2.db? is in use and will not be installed > Warning message: > installed directory not writable, cannot update packages 'boot', > 'class', > 'cluster', 'foreign', 'KernSmooth', 'MASS', 'Matrix', 'mgcv', 'nlme', > 'nnet', > 'rpart', 'spatial' > > Regards > Rabia > > -----Original Message----- > From: Dan Tenenbaum [mailto:dtenenba at fhcrc.org] > Sent: 02 April 2014 07:19 PM > To: Rabia Johnson > Cc: bioconductor at r-project.org > Subject: Re: [BioC] BiocLite eror > > > > ----- Original Message ----- > > From: "Rabia Johnson" <rabia.johnson at="" mrc.ac.za=""> > > To: bioconductor at r-project.org > > Sent: Wednesday, April 2, 2014 12:04:19 AM > > Subject: [BioC] BiocLite eror > > > > HI, > > > > Object : problem with hgu133plus2.db you need to install this > > package > > to complete this step > > > > If possible can anyone help. I am new to R and are working through > > the > > tutorial of Daniel Swan (Analysing microarray data in > > BioConductor) > > Upon writing the following command I get the following error: > > > > > biocLite("hgu133plus2.db") > > BioC_mirror: http://bioconductor.org > > Using Bioconductor version 2.13 (BiocInstaller 1.12.0), R version > > 3.0.3. > > Installing package(s) 'hgu133plus2.db' > > Warning: package 'hgu133plus2.db' is in use and will not be > > installed > > Warning message: > > installed directory not writable, cannot update packages 'boot', > > 'class', > > 'cluster', 'foreign', 'KernSmooth', 'MASS', 'Matrix', 'mgcv', > > 'nlme', 'nnet', > > 'rpart', 'spatial' > > > > > > Try quitting your R session and starting a fresh one like this: > > R --vanilla > > And then running > > > source("http://bioconductor.org/biocLite.R") > biocLite("hgu133plus2.db") > > > Does that work? > > Dan > > > > > Thus, needless to say when I continue with the next command I get > > more > > errors: > > > > > library(hgu133plus2.db) > > > library(annotate) > > > gene.symbols <- getSYMBOL(probeset.list$ID, "hgu133plus2") > > Error in unlist(lookUp(x, data, "SYMBOL")) : > > error in evaluating the argument 'x' in selecting a method for > > function 'unlist': Error in lookUp(x, data, "SYMBOL") : No keys > > provided > > > > > > Can anyone help please > > Regards > > Rabia > > > > > > _______________________________________ > > Rabia Johnson (PhD) > > Senior Scientist > > South African Medical Research Council Diabetes Discovery Platform > > Building E Francie van Zijl Drive, Parow Valley, 7505, Cape Town > > Cell: +27 82 0677296 > > Tel: +27 21 938 0866 > > Fax: +27 21 938 0456 > > E-mail: rabia.johnson at mrc.ac.za > > > > > > Disclaimer\ \ The information contained in this > > communic...{{dropped:20}} > > > > _______________________________________________ > > 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 > > > > > > > Disclaimer > > The information contained in this communication from the sender is > confidential. 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