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Question: how to install gnGNF1a cdf and probe files to a recent version of R (2.13.1)?
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gravatar for Nicholas Wong
6.0 years ago by
Nicholas Wong30 wrote:
Hi all, first time poster long time reader. I am trying to download and reanalyse publicly available gene expression sets that have used the custom U133A arrays that require the gnGNF1a library. I have attached the error message and sessionInfo() below, but it would seem one can not install these libraries into the R 2.13.1, I have tried sourcing the library from a website and installing manually and the error as you can see is that it is not a valid installed package. I think I would need to install an older version of R to accommodate for this, does anyone know what version this is? cheers nick > expData <- ReadAffy() > expData AffyBatch object size of arrays=712x712 features (19 kb) cdf=gnGNF1Ba (??? affyids) number of samples=8 Error in function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE, : 'gngnf1bacdf' is not a valid installed package In addition: Warning message: missing cdf environment! in show(AffyBatch) > sessionInfo() R version 2.13.1 (2011-07-08) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/en_US.UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affy_1.30.0 Biobase_2.12.2 loaded via a namespace (and not attached): [1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.1 Dr Nick Wong BSc(Hons), Ph.D Postdoctoral Fellow Cancer and Disease Epigenetics, Early Development and Disease Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road Parkville Victoria 3052 Australia T 9936 6621 F 9348 1391 M 0421 030 482 E nick.wong@mcri.edu.au www.mcri.edu.au This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.  Please consider the environment before printing this email ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ [[alternative HTML version deleted]]
ADD COMMENTlink modified 6.0 years ago by James W. MacDonald45k • written 6.0 years ago by Nicholas Wong30
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gravatar for James W. MacDonald
6.0 years ago by
United States
James W. MacDonald45k wrote:
Hi Nicholas, On 12/5/2011 10:39 PM, Nicholas Wong wrote: > Hi all, first time poster long time reader. > > I am trying to download and reanalyse publicly available gene expression sets that have used the custom U133A arrays that require the gnGNF1a library. > > I have attached the error message and sessionInfo() below, but it would seem one can not install these libraries into the R 2.13.1, I have tried sourcing the library from a website and installing manually and the error as you can see is that it is not a valid installed package. > > I think I would need to install an older version of R to accommodate for this, does anyone know what version this is? It's not an issue of the R version; instead it is an issue with that particular chip. We (meaning BioC) only create cdf and probe packages for Affy chips for which we can get the underlying data directly from Affymetrix. This necessarily excludes all custom chips, as Affymetrix have never to my knowledge made any custom chip data available. The researchers who originally ran those chips may still have the cdf and probe data files, and may be willing to give them to you. If so, you can create your own cdf and probe packages using the makecdfenv and AnnotationDbi packages, respectively. Best, Jim > > cheers > > nick > > >> expData<- ReadAffy() >> expData > AffyBatch object > size of arrays=712x712 features (19 kb) > cdf=gnGNF1Ba (??? affyids) > number of samples=8 > Error in function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE, : > 'gngnf1bacdf' is not a valid installed package > In addition: Warning message: > missing cdf environment! in show(AffyBatch) >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C/en_US.UTF-8/C/C/C/C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affy_1.30.0 Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.1 > > > > Dr Nick Wong BSc(Hons), Ph.D > Postdoctoral Fellow > Cancer and Disease Epigenetics, Early Development and Disease > > Murdoch Childrens Research Institute > The Royal ChildrenâEUR^(TM)s Hospital > Flemington Road Parkville Victoria 3052 Australia > T 9936 6621 F 9348 1391 > M 0421 030 482 > E nick.wong@mcri.edu.au > www.mcri.edu.au > > > > This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. > > ï?? Please consider the environment before printing this email > > > > > > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > ______________________________________________________________________ > [[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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues [[alternative HTML version deleted]]
ADD COMMENTlink written 6.0 years ago by James W. MacDonald45k
Hi, FYI: I am almost 100% certain that the array you are looking for is available under platform accession number GPL1074. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL1074 You can download the CDF and probe files to create the R-compliant packages yourselves. Note that this array is 'officially' called the GNF1H array. http://biogps.org/downloads/ In addition, the folks at the MBNI provide remapped CDFs (also as R packages) for this array that are build using current genome annotation information. HTH, Guido --------------------------------------------------------- Guido Hooiveld, PhD Nutrition, Metabolism & Genomics Group Division of Human Nutrition Wageningen University Biotechnion, Bomenweg 2 NL-6703 HD Wageningen the Netherlands tel: (+)31 317 485788 fax: (+)31 317 483342 email: guido.hooiveld at wur.nl internet: http://nutrigene.4t.com http://scholar.google.com/citations?user=qFHaMnoAAAAJ http://www.researcherid.com/rid/F-4912-2010 -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of James W. MacDonald Sent: Thursday, December 08, 2011 15:21 To: Nicholas Wong Cc: bioconductor at r-project.org Subject: Re: [BioC] how to install gnGNF1a cdf and probe files to a recent version of R (2.13.1)? Hi Nicholas, On 12/5/2011 10:39 PM, Nicholas Wong wrote: > Hi all, first time poster long time reader. > > I am trying to download and reanalyse publicly available gene expression sets that have used the custom U133A arrays that require the gnGNF1a library. > > I have attached the error message and sessionInfo() below, but it would seem one can not install these libraries into the R 2.13.1, I have tried sourcing the library from a website and installing manually and the error as you can see is that it is not a valid installed package. > > I think I would need to install an older version of R to accommodate for this, does anyone know what version this is? It's not an issue of the R version; instead it is an issue with that particular chip. We (meaning BioC) only create cdf and probe packages for Affy chips for which we can get the underlying data directly from Affymetrix. This necessarily excludes all custom chips, as Affymetrix have never to my knowledge made any custom chip data available. The researchers who originally ran those chips may still have the cdf and probe data files, and may be willing to give them to you. If so, you can create your own cdf and probe packages using the makecdfenv and AnnotationDbi packages, respectively. Best, Jim > > cheers > > nick > > >> expData<- ReadAffy() >> expData > AffyBatch object > size of arrays=712x712 features (19 kb) cdf=gnGNF1Ba (??? affyids) > number of samples=8 Error in function (package, help, pos = 2, lib.loc > = NULL, character.only = FALSE, : > 'gngnf1bacdf' is not a valid installed package In addition: Warning > message: > missing cdf environment! in show(AffyBatch) >> sessionInfo() > R version 2.13.1 (2011-07-08) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C/en_US.UTF-8/C/C/C/C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affy_1.30.0 Biobase_2.12.2 > > loaded via a namespace (and not attached): > [1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.1 > > > > Dr Nick Wong BSc(Hons), Ph.D > Postdoctoral Fellow > Cancer and Disease Epigenetics, Early Development and Disease > > Murdoch Childrens Research Institute > The Royal Children?EUR^(TM)s Hospital > Flemington Road Parkville Victoria 3052 Australia T 9936 6621 F 9348 > 1391 M 0421 030 482 E nick.wong at mcri.edu.au www.mcri.edu.au > > > > This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. > > ??? Please consider the environment before printing this email > > > > > > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > ______________________________________________________________________ > [[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 Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by Guido Hooiveld2.2k
Jim, thanks for your reply, I think I have found these cdf and probe files and will have a go at creating custom packages using makecdfenv. cheers nick Dr Nick Wong BSc(Hons), Ph.D Postdoctoral Fellow Cancer and Disease Epigenetics, Early Development and Disease Murdoch Childrens Research Institute The Royal Children’s Hospital Flemington Road Parkville Victoria 3052 Australia T 9936 6621 F 9348 1391 M 0421 030 482 E nick.wong@mcri.edu.au www.mcri.edu.au This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication.  Please consider the environment before printing this email On 09/12/2011, at 1:21 AM, James W. MacDonald wrote: > Hi Nicholas, > > On 12/5/2011 10:39 PM, Nicholas Wong wrote: >> >> Hi all, first time poster long time reader. >> >> I am trying to download and reanalyse publicly available gene expression sets that have used the custom U133A arrays that require the gnGNF1a library. >> >> I have attached the error message and sessionInfo() below, but it would seem one can not install these libraries into the R 2.13.1, I have tried sourcing the library from a website and installing manually and the error as you can see is that it is not a valid installed package. >> >> I think I would need to install an older version of R to accommodate for this, does anyone know what version this is? > > It's not an issue of the R version; instead it is an issue with that particular chip. We (meaning BioC) only create cdf and probe packages for Affy chips for which we can get the underlying data directly from Affymetrix. This necessarily excludes all custom chips, as Affymetrix have never to my knowledge made any custom chip data available. > > The researchers who originally ran those chips may still have the cdf and probe data files, and may be willing to give them to you. If so, you can create your own cdf and probe packages using the makecdfenv and AnnotationDbi packages, respectively. > > Best, > > Jim > > >> >> cheers >> >> nick >> >> >>> expData <- ReadAffy() >>> expData >> AffyBatch object >> size of arrays=712x712 features (19 kb) >> cdf=gnGNF1Ba (??? affyids) >> number of samples=8 >> Error in function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE, : >> 'gngnf1bacdf' is not a valid installed package >> In addition: Warning message: >> missing cdf environment! in show(AffyBatch) >>> sessionInfo() >> R version 2.13.1 (2011-07-08) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] C/en_US.UTF-8/C/C/C/C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] affy_1.30.0 Biobase_2.12.2 >> >> loaded via a namespace (and not attached): >> [1] affyio_1.20.0 preprocessCore_1.14.0 tools_2.13.1 >> >> >> >> Dr Nick Wong BSc(Hons), Ph.D >> Postdoctoral Fellow >> Cancer and Disease Epigenetics, Early Development and Disease >> >> Murdoch Childrens Research Institute >> The Royal Children’s Hospital >> Flemington Road Parkville Victoria 3052 Australia >> T 9936 6621 F 9348 1391 >> M 0421 030 482 >> E nick.wong@mcri.edu.au >> www.mcri.edu.au >> >> >> >> This e-mail and any attachments to it (the "Communication") are, unless otherwise stated, confidential, may contain copyright material and is for the use only of the intended recipient. If you receive the Communication in error, please notify the sender immediately by return e-mail, delete the Communication and the return e-mail, and do not read, copy, retransmit or otherwise deal with it. Any views expressed in the Communication are those of the individual sender only, unless expressly stated to be those of Murdoch Childrens Research Institute (MCRI) ABN 21 006 566 972 or any of its related entities. MCRI does not accept liability in connection with the integrity of or errors in the Communication, computer virus, data corruption, interference or delay arising from or in respect of the Communication. >> >>  Please consider the environment before printing this email >> >> >> >> >> >> >> ______________________________________________________________________ >> This email has been scanned by the Symantec Email Security.cloud service. >> For more information please visit http://www.symanteccloud.com >> ______________________________________________________________________ >> [[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 > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > > If you have any question, please contact MCRI IT Helpdesk for further assistance. > ______________________________________________________________________ ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ [[alternative HTML version deleted]]
ADD REPLYlink written 6.0 years ago by Nicholas Wong30
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