Thanks for the suggestions. I have updated to R 2.2.1. I have tried biocLite and get the following error when running QCReport: Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about chip type: porcinecdf Error in plot(qc(object)) : unable to find the argument 'x' in selecting a method for function 'plot' Any suggestions? > > On Mar 30, 2006, at 3:21 PM, David Carter wrote: > >> Hello, >> I am getting some errors using the affy library with porcine arrays: >> Error in getCdfInfo(object) : Could not obtain CDF environment, >> problems >> encountered: >> Specified environment specified did not contain Porcine >> Library - package porcinecdf not installed >> Data for package affy did not contain Porcine >> Bioconductor - porcinecdf not available >> In addition: Warning message: >> Failed to read replisting at >> http://www.bioconductor.org/repository/devel/package/Win32 in: >> getReplisting(repURL, repFile, method = method) >> >> I am using R version 2.0.1. How do I get the porcine CDF installed? > > > That is really old. You should update, espcially because newer > version of affy/Bioconductor will not work with R this old. > > Anyway, try > source("http://www.bioconductor.org/biocLite.R") > biocLite("porcinecdf") > > /Kasper > > > >> >> -- >> David Carter >> London Regional Genomics Centre >> Robarts Research Institute, Room 4.01 >> PO Box 5015, 100 Perth Drive >> London, Ontario, Canada, N6A 5K8 >> >> phone: (519) 663-3253 >> fax: (519) 663-3037 >> >> dcarter at robarts.ca >> http://www.lrgc.ca >> >> _______________________________________________ >> 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 > > -- David Carter London Regional Genomics Centre Robarts Research Institute, Room 4.01 PO Box 5015, 100 Perth Drive London, Ontario, Canada, N6A 5K8 phone: (519) 663-3253 fax: (519) 663-3037 dcarter at robarts.ca http://www.lrgc.ca > > On Mar 30, 2006, at 3:21 PM, David Carter wrote: > >> Hello, >> I am getting some errors using the affy library with porcine arrays: >> Error in getCdfInfo(object) : Could not obtain CDF environment, >> problems >> encountered: >> Specified environment specified did not contain Porcine >> Library - package porcinecdf not installed >> Data for package affy did not contain Porcine >> Bioconductor - porcinecdf not available >> In addition: Warning message: >> Failed to read replisting at >> http://www.bioconductor.org/repository/devel/package/Win32 in: >> getReplisting(repURL, repFile, method = method) >> >> I am using R version 2.0.1. How do I get the porcine CDF installed? > > > That is really old. You should update, espcially because newer > version of affy/Bioconductor will not work with R this old. > > Anyway, try > source("http://www.bioconductor.org/biocLite.R") > biocLite("porcinecdf") > > /Kasper > > > >> >> -- >> David Carter >> London Regional Genomics Centre >> Robarts Research Institute, Room 4.01 >> PO Box 5015, 100 Perth Drive >> London, Ontario, Canada, N6A 5K8 >> >> phone: (519) 663-3253 >> fax: (519) 663-3037 >> >> dcarter at robarts.ca >> http://www.lrgc.ca >> >> _______________________________________________ >> 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 > > -- David Carter London Regional Genomics Centre Robarts Research Institute, Room 4.01 PO Box 5015, 100 Perth Drive London, Ontario, Canada, N6A 5K8 phone: (519) 663-3253 fax: (519) 663-3037 dcarter at robarts.ca http://www.lrgc.ca > > On Mar 30, 2006, at 3:21 PM, David Carter wrote: > >> Hello, >> I am getting some errors using the affy library with porcine arrays: >> Error in getCdfInfo(object) : Could not obtain CDF environment, >> problems >> encountered: >> Specified environment specified did not contain Porcine >> Library - package porcinecdf not installed >> Data for package affy did not contain Porcine >> Bioconductor - porcinecdf not available >> In addition: Warning message: >> Failed to read replisting at >> http://www.bioconductor.org/repository/devel/package/Win32 in: >> getReplisting(repURL, repFile, method = method) >> >> I am using R version 2.0.1. How do I get the porcine CDF installed? > > > That is really old. You should update, espcially because newer > version of affy/Bioconductor will not work with R this old. > > Anyway, try > source("http://www.bioconductor.org/biocLite.R") > biocLite("porcinecdf") > > /Kasper > > > >> >> -- >> David Carter >> London Regional Genomics Centre >> Robarts Research Institute, Room 4.01 >> PO Box 5015, 100 Perth Drive >> London, Ontario, Canada, N6A 5K8 >> >> phone: (519) 663-3253 >> fax: (519) 663-3037 >> >> dcarter at robarts.ca >> http://www.lrgc.ca >> >> _______________________________________________ >> 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 > > -- David Carter London Regional Genomics Centre Robarts Research Institute, Room 4.01 PO Box 5015, 100 Perth Drive London, Ontario, Canada, N6A 5K8 phone: (519) 663-3253 fax: (519) 663-3037 dcarter at robarts.ca http://www.lrgc.ca

David Carter wrote: > Thanks for the suggestions. > > I have updated to R 2.2.1. I have tried biocLite and get the following > error when running QCReport: > Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about > chip type: porcinecdf > Error in plot(qc(object)) : unable to find the argument 'x' in selecting > a method for function 'plot' > > Any suggestions? This error indicates that simpleaffy doesn't contain the QC parameters for this particular chip, so for now you won't be able to do the QC stuff. You might contact the maintainer (Crispin Miller) directly to see if they can be added. Best, Jim > > >>On Mar 30, 2006, at 3:21 PM, David Carter wrote: >> >> >>>Hello, >>>I am getting some errors using the affy library with porcine arrays: >>>Error in getCdfInfo(object) : Could not obtain CDF environment, >>>problems >>>encountered: >>>Specified environment specified did not contain Porcine >>>Library - package porcinecdf not installed >>>Data for package affy did not contain Porcine >>>Bioconductor - porcinecdf not available >>>In addition: Warning message: >>>Failed to read replisting at >>>http://www.bioconductor.org/repository/devel/package/Win32 in: >>>getReplisting(repURL, repFile, method = method) >>> >>>I am using R version 2.0.1. How do I get the porcine CDF installed? >> >> >>That is really old. You should update, espcially because newer >>version of affy/Bioconductor will not work with R this old. >> >>Anyway, try >> source("http://www.bioconductor.org/biocLite.R") >> biocLite("porcinecdf") >> >>/Kasper >> >> >> >> >>>-- >>>David Carter >>>London Regional Genomics Centre >>>Robarts Research Institute, Room 4.01 >>>PO Box 5015, 100 Perth Drive >>>London, Ontario, Canada, N6A 5K8 >>> >>>phone: (519) 663-3253 >>>fax: (519) 663-3037 >>> >>>dcarter at robarts.ca >>>http://www.lrgc.ca >>> >>>_______________________________________________ >>>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.

Thanks Craig, I believe I altered the 3 files with the correct information, but now am getting this error: Error in FUN(X[[4]], ...) : subscript out of bounds Error in plot(qc(object)) : unable to find the argument 'x' in selecting a method for function 'plot' You suggested to use an array with the same number of features, but don't all the Affy arrays have different numbers of features? Please correct me if I am wrong. I copied and altered the last line which was a Rat array. This error looks like I am telling it the wrong number of features. Any suggestions on where I can correct this? Sincerely, David Carter Craig Parman wrote: > David, > > If look in the ../library/simpleaffy/data directory there are three > files that contain the qc parameters. You should be able to add a > line to each to get the package working until it is updated. I would > copy a line from a different array with the sample number of features > and modify the cdf name to "porcinecdf" For the spikes and qc.probes > files just change the probeset names for the controls to match array > data. That should get it working. > > btw - make a backup of the files before you change them. > > > Craig > > > > ----- Original Message ----- From: "David Carter" <dcarter at="" robarts.ca=""> > To: "Bioconductor list serv" <bioconductor at="" stat.math.ethz.ch=""> > Sent: Tuesday, April 11, 2006 1:05 PM > Subject: Re: [BioC] affy package and porcine arrays > > >> Thanks for the suggestions. >> >> I have updated to R 2.2.1. I have tried biocLite and get the following >> error when running QCReport: >> Error in qc.affy(unnormalised, ...) : I'm sorry, I do not know about >> chip type: porcinecdf >> Error in plot(qc(object)) : unable to find the argument 'x' in selecting >> a method for function 'plot' >> >> Any suggestions? >> >>> >>> On Mar 30, 2006, at 3:21 PM, David Carter wrote: >>> >>>> Hello, >>>> I am getting some errors using the affy library with porcine arrays: >>>> Error in getCdfInfo(object) : Could not obtain CDF environment, >>>> problems >>>> encountered: >>>> Specified environment specified did not contain Porcine >>>> Library - package porcinecdf not installed >>>> Data for package affy did not contain Porcine >>>> Bioconductor - porcinecdf not available >>>> In addition: Warning message: >>>> Failed to read replisting at >>>> http://www.bioconductor.org/repository/devel/package/Win32 in: >>>> getReplisting(repURL, repFile, method = method) >>>> >>>> I am using R version 2.0.1. How do I get the porcine CDF installed? >>> >>> >>> >>> That is really old. You should update, espcially because newer >>> version of affy/Bioconductor will not work with R this old. >>> >>> Anyway, try >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite("porcinecdf") >>> >>> /Kasper >>> >>> >>> >>>> >>>> -- >>>> David Carter >>>> London Regional Genomics Centre >>>> Robarts Research Institute, Room 4.01 >>>> PO Box 5015, 100 Perth Drive >>>> London, Ontario, Canada, N6A 5K8 >>>> >>>> phone: (519) 663-3253 >>>> fax: (519) 663-3037 >>>> >>>> dcarter at robarts.ca >>>> http://www.lrgc.ca >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >> >> -- >> David Carter >> London Regional Genomics Centre >> Robarts Research Institute, Room 4.01 >> PO Box 5015, 100 Perth Drive >> London, Ontario, Canada, N6A 5K8 >> >> phone: (519) 663-3253 >> fax: (519) 663-3037 >> >> dcarter at robarts.ca >> http://www.lrgc.ca >> >> >>> >>> On Mar 30, 2006, at 3:21 PM, David Carter wrote: >>> >>>> Hello, >>>> I am getting some errors using the affy library with porcine arrays: >>>> Error in getCdfInfo(object) : Could not obtain CDF environment, >>>> problems >>>> encountered: >>>> Specified environment specified did not contain Porcine >>>> Library - package porcinecdf not installed >>>> Data for package affy did not contain Porcine >>>> Bioconductor - porcinecdf not available >>>> In addition: Warning message: >>>> Failed to read replisting at >>>> http://www.bioconductor.org/repository/devel/package/Win32 in: >>>> getReplisting(repURL, repFile, method = method) >>>> >>>> I am using R version 2.0.1. How do I get the porcine CDF installed? >>> >>> >>> >>> That is really old. You should update, espcially because newer >>> version of affy/Bioconductor will not work with R this old. >>> >>> Anyway, try >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite("porcinecdf") >>> >>> /Kasper >>> >>> >>> >>>> >>>> -- >>>> David Carter >>>> London Regional Genomics Centre >>>> Robarts Research Institute, Room 4.01 >>>> PO Box 5015, 100 Perth Drive >>>> London, Ontario, Canada, N6A 5K8 >>>> >>>> phone: (519) 663-3253 >>>> fax: (519) 663-3037 >>>> >>>> dcarter at robarts.ca >>>> http://www.lrgc.ca >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >> >> -- >> David Carter >> London Regional Genomics Centre >> Robarts Research Institute, Room 4.01 >> PO Box 5015, 100 Perth Drive >> London, Ontario, Canada, N6A 5K8 >> >> phone: (519) 663-3253 >> fax: (519) 663-3037 >> >> dcarter at robarts.ca >> http://www.lrgc.ca >> >> >>> >>> On Mar 30, 2006, at 3:21 PM, David Carter wrote: >>> >>>> Hello, >>>> I am getting some errors using the affy library with porcine arrays: >>>> Error in getCdfInfo(object) : Could not obtain CDF environment, >>>> problems >>>> encountered: >>>> Specified environment specified did not contain Porcine >>>> Library - package porcinecdf not installed >>>> Data for package affy did not contain Porcine >>>> Bioconductor - porcinecdf not available >>>> In addition: Warning message: >>>> Failed to read replisting at >>>> http://www.bioconductor.org/repository/devel/package/Win32 in: >>>> getReplisting(repURL, repFile, method = method) >>>> >>>> I am using R version 2.0.1. How do I get the porcine CDF installed? >>> >>> >>> >>> That is really old. You should update, espcially because newer >>> version of affy/Bioconductor will not work with R this old. >>> >>> Anyway, try >>> source("http://www.bioconductor.org/biocLite.R") >>> biocLite("porcinecdf") >>> >>> /Kasper >>> >>> >>> >>>> >>>> -- >>>> David Carter >>>> London Regional Genomics Centre >>>> Robarts Research Institute, Room 4.01 >>>> PO Box 5015, 100 Perth Drive >>>> London, Ontario, Canada, N6A 5K8 >>>> >>>> phone: (519) 663-3253 >>>> fax: (519) 663-3037 >>>> >>>> dcarter at robarts.ca >>>> http://www.lrgc.ca >>>> >>>> _______________________________________________ >>>> 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 >>> >>> >>> >> >> -- >> David Carter >> London Regional Genomics Centre >> Robarts Research Institute, Room 4.01 >> PO Box 5015, 100 Perth Drive >> London, Ontario, Canada, N6A 5K8 >> >> phone: (519) 663-3253 >> fax: (519) 663-3037 >> >> dcarter at robarts.ca >> http://www.lrgc.ca >> >> _______________________________________________ >> 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 > > -- David Carter London Regional Genomics Centre Robarts Research Institute, Room 4.01 PO Box 5015, 100 Perth Drive London, Ontario, Canada, N6A 5K8 phone: (519) 663-3253 fax: (519) 663-3037 dcarter at robarts.ca http://www.lrgc.ca