ERCC spike-in probes in
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Hi team, I'm part of the lab that made everyone's microarray analysis more difficult by demanding everyone do ERCC spike-in normalization. Unfortunately, the primeviewcdf does not automatically contain the probeset IDs for ERCCs, despite the probes being physically on the chip. We've worked with Affy to get a custom cdf made that contains the locations of the ERCC probes on the primeview chip. Would you be interested in folding this into your code so that more people can benefit from it? -- output of sessionInfo(): > sessionInfo() R version 3.0.1 (2013-05-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] makecdfenv_1.36.0 affyio_1.28.0 affy_1.38.1 Biobase_2.20.0 [5] BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] BiocInstaller_1.10.2 preprocessCore_1.22.0 tools_3.0.1 [4] zlibbioc_1.6.0 -- Sent via the guest posting facility at bioconductor.org.
Microarray Normalization cdf affy Microarray Normalization cdf affy • 2.0k views
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@james-w-macdonald-5106
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Hi Brian, Sure. You can send it directly to me. Best, Jim On 6/24/2013 3:33 PM, Brian Abraham [guest] wrote: > Hi team, > > I'm part of the lab that made everyone's microarray analysis more difficult by demanding everyone do ERCC spike-in normalization. Unfortunately, the primeviewcdf does not automatically contain the probeset IDs for ERCCs, despite the probes being physically on the chip. We've worked with Affy to get a custom cdf made that contains the locations of the ERCC probes on the primeview chip. Would you be interested in folding this into your code so that more people can benefit from it? > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] makecdfenv_1.36.0 affyio_1.28.0 affy_1.38.1 Biobase_2.20.0 > [5] BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] BiocInstaller_1.10.2 preprocessCore_1.22.0 tools_3.0.1 > [4] zlibbioc_1.6.0 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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
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Hi Brian, I am not going to build this package for the current version of Bioconductor, but it will appear in the next release. Please note that I have replaced the 'stock' Affymetrix cdf with this one, so people will automatically get the cdf that contains the ERCC probe mappings (e.g., this cdf package will be called 'primeviewcdf', just like the current one, but will contain the ERCC probes as well). Best, Jim On 6/24/2013 6:26 PM, Brian J. Abraham wrote: > Hi Jim, > > The CDF is publicly available via GEO. If this doesn't work, I can > find another way to get it to you. Thanks for taking this on! > > http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16043 > > ~Brian J. Abraham > Postdoctoral Associate > Lab of Richard Young > Whitehead Institute for Biomedical Research > Nine Cambridge Center > Cambridge, MA 02142 > > > On Mon, Jun 24, 2013 at 5:14 PM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Brian, > > Sure. You can send it directly to me. > > Best, > > Jim > > > > > On 6/24/2013 3:33 PM, Brian Abraham [guest] wrote: > > Hi team, > > I'm part of the lab that made everyone's microarray analysis > more difficult by demanding everyone do ERCC spike-in > normalization. Unfortunately, the primeviewcdf does not > automatically contain the probeset IDs for ERCCs, despite the > probes being physically on the chip. We've worked with Affy > to get a custom cdf made that contains the locations of the > ERCC probes on the primeview chip. Would you be interested in > folding this into your code so that more people can benefit > from it? > > -- output of sessionInfo(): > > sessionInfo() > > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods > [8] base > > other attached packages: > [1] makecdfenv_1.36.0 affyio_1.28.0 affy_1.38.1 > Biobase_2.20.0 > [5] BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] BiocInstaller_1.10.2 preprocessCore_1.22.0 tools_3.0.1 > [4] zlibbioc_1.6.0 > > -- > Sent via the guest posting facility at bioconductor.org > <http: bioconductor.org="">. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto: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 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
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Hi, Out of curiosity: After reading this I just wondered whether the ERCC probes are unique for the primeview array, or are they also included in other Affymetrix array designs? [In addition to the "standard" Dap, Thr, Phe and Lys -PolyA spikes I know of]. Thanks, 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: Tuesday, June 25, 2013 16:26 To: Brian J. Abraham Cc: Bioconductor at r-project.org Subject: Re: [BioC] ERCC spike-in probes in Hi Brian, I am not going to build this package for the current version of Bioconductor, but it will appear in the next release. Please note that I have replaced the 'stock' Affymetrix cdf with this one, so people will automatically get the cdf that contains the ERCC probe mappings (e.g., this cdf package will be called 'primeviewcdf', just like the current one, but will contain the ERCC probes as well). Best, Jim On 6/24/2013 6:26 PM, Brian J. Abraham wrote: > Hi Jim, > > The CDF is publicly available via GEO. If this doesn't work, I can > find another way to get it to you. Thanks for taking this on! > > http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16043 > > ~Brian J. Abraham > Postdoctoral Associate > Lab of Richard Young > Whitehead Institute for Biomedical Research Nine Cambridge Center > Cambridge, MA 02142 > > > On Mon, Jun 24, 2013 at 5:14 PM, James W. MacDonald <jmacdon at="" uw.edu=""> <mailto:jmacdon at="" uw.edu="">> wrote: > > Hi Brian, > > Sure. You can send it directly to me. > > Best, > > Jim > > > > > On 6/24/2013 3:33 PM, Brian Abraham [guest] wrote: > > Hi team, > > I'm part of the lab that made everyone's microarray analysis > more difficult by demanding everyone do ERCC spike-in > normalization. Unfortunately, the primeviewcdf does not > automatically contain the probeset IDs for ERCCs, despite the > probes being physically on the chip. We've worked with Affy > to get a custom cdf made that contains the locations of the > ERCC probes on the primeview chip. Would you be interested in > folding this into your code so that more people can benefit > from it? > > -- output of sessionInfo(): > > sessionInfo() > > R version 3.0.1 (2013-05-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] parallel stats graphics grDevices utils datasets > methods > [8] base > > other attached packages: > [1] makecdfenv_1.36.0 affyio_1.28.0 affy_1.38.1 > Biobase_2.20.0 > [5] BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] BiocInstaller_1.10.2 preprocessCore_1.22.0 tools_3.0.1 > [4] zlibbioc_1.6.0 > > -- > Sent via the guest posting facility at bioconductor.org > <http: bioconductor.org="">. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto: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 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 _______________________________________________ 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
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Hi team, According to our microarray guru, the older arrays like U133 or mouse 430 do not have the ERCC probes, but some of the newer designs like Primeview and maybe GeneST might have them. Going forward, I think it's safe to expect Affy to put the ERCC probes onto their new chips. Jim, thanks again. Do you know when the new package will be released into the wild? Would it be possible to get a beta version of it for our in-house usage if it's a long ways off? ~Brian On Tue, Jun 25, 2013 at 12:08 PM, Hooiveld, Guido <guido.hooiveld@wur.nl>wrote: > Hi, > Out of curiosity: > After reading this I just wondered whether the ERCC probes are unique for > the primeview array, or are they also included in other Affymetrix array > designs? > [In addition to the "standard" Dap, Thr, Phe and Lys -PolyA spikes I know > of]. > > Thanks, > 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@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: Tuesday, June 25, 2013 16:26 > To: Brian J. Abraham > Cc: Bioconductor@r-project.org > Subject: Re: [BioC] ERCC spike-in probes in > > Hi Brian, > > I am not going to build this package for the current version of > Bioconductor, but it will appear in the next release. Please note that I > have replaced the 'stock' Affymetrix cdf with this one, so people will > automatically get the cdf that contains the ERCC probe mappings (e.g., this > cdf package will be called 'primeviewcdf', just like the current one, but > will contain the ERCC probes as well). > > Best, > > Jim > > > > On 6/24/2013 6:26 PM, Brian J. Abraham wrote: > > Hi Jim, > > > > The CDF is publicly available via GEO. If this doesn't work, I can > > find another way to get it to you. Thanks for taking this on! > > > > http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16043 > > > > ~Brian J. Abraham > > Postdoctoral Associate > > Lab of Richard Young > > Whitehead Institute for Biomedical Research Nine Cambridge Center > > Cambridge, MA 02142 > > > > > > On Mon, Jun 24, 2013 at 5:14 PM, James W. MacDonald <jmacdon@uw.edu> > <mailto:jmacdon@uw.edu>> wrote: > > > > Hi Brian, > > > > Sure. You can send it directly to me. > > > > Best, > > > > Jim > > > > > > > > > > On 6/24/2013 3:33 PM, Brian Abraham [guest] wrote: > > > > Hi team, > > > > I'm part of the lab that made everyone's microarray analysis > > more difficult by demanding everyone do ERCC spike-in > > normalization. Unfortunately, the primeviewcdf does not > > automatically contain the probeset IDs for ERCCs, despite the > > probes being physically on the chip. We've worked with Affy > > to get a custom cdf made that contains the locations of the > > ERCC probes on the primeview chip. Would you be interested in > > folding this into your code so that more people can benefit > > from it? > > > > -- output of sessionInfo(): > > > > sessionInfo() > > > > R version 3.0.1 (2013-05-16) > > Platform: x86_64-pc-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=C LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] parallel stats graphics grDevices utils datasets > > methods > > [8] base > > > > other attached packages: > > [1] makecdfenv_1.36.0 affyio_1.28.0 affy_1.38.1 > > Biobase_2.20.0 > > [5] BiocGenerics_0.6.0 > > > > loaded via a namespace (and not attached): > > [1] BiocInstaller_1.10.2 preprocessCore_1.22.0 tools_3.0.1 > > [4] zlibbioc_1.6.0 > > > > -- > > Sent via the guest posting facility at bioconductor.org > > <http: bioconductor.org="">. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org <mailto: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 > > University of Washington > > Environmental and Occupational Health Sciences > > 4225 Roosevelt Way NE, # 100 > > Seattle WA 98105-6099 > > > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > _______________________________________________ > 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]]
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Hi Brian, The next release is in October. And you don't need me to give you the package. Just get the cdf from GEO, ungzip it, rename the file PrimeView.cdf, and then biocLite("makecdfenv") library(makecdfenv) make.cdf.package("PrimeView.cdf", species="Homo_sapiens", version = "12.1") install.packages("primeviewcdf/", repos = NULL, type = "source") And you will be in business. Best, Jim On 6/25/2013 3:06 PM, Brian J. Abraham wrote: > Hi team, > > According to our microarray guru, the older arrays like U133 or mouse > 430 do not have the ERCC probes, but some of the newer designs like > Primeview and maybe GeneST might have them. Going forward, I think > it's safe to expect Affy to put the ERCC probes onto their new chips. > > Jim, thanks again. Do you know when the new package will be released > into the wild? Would it be possible to get a beta version of it for > our in-house usage if it's a long ways off? > > ~Brian > > > On Tue, Jun 25, 2013 at 12:08 PM, Hooiveld, Guido > <guido.hooiveld at="" wur.nl="" <mailto:guido.hooiveld="" at="" wur.nl="">> wrote: > > Hi, > Out of curiosity: > After reading this I just wondered whether the ERCC probes are > unique for the primeview array, or are they also included in other > Affymetrix array designs? > [In addition to the "standard" Dap, Thr, Phe and Lys -PolyA spikes > I know of]. > > Thanks, > 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 <mailto: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 at r-project.org > <mailto:bioconductor-bounces at="" r-project.org=""> > [mailto:bioconductor-bounces at r-project.org > <mailto:bioconductor-bounces at="" r-project.org="">] On Behalf Of James W. > MacDonald > Sent: Tuesday, June 25, 2013 16:26 > To: Brian J. Abraham > Cc: Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > Subject: Re: [BioC] ERCC spike-in probes in > > Hi Brian, > > I am not going to build this package for the current version of > Bioconductor, but it will appear in the next release. Please note > that I have replaced the 'stock' Affymetrix cdf with this one, so > people will automatically get the cdf that contains the ERCC probe > mappings (e.g., this cdf package will be called 'primeviewcdf', > just like the current one, but will contain the ERCC probes as well). > > Best, > > Jim > > > > On 6/24/2013 6:26 PM, Brian J. Abraham wrote: > > Hi Jim, > > > > The CDF is publicly available via GEO. If this doesn't work, I can > > find another way to get it to you. Thanks for taking this on! > > > > http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL16043 > > > > ~Brian J. Abraham > > Postdoctoral Associate > > Lab of Richard Young > > Whitehead Institute for Biomedical Research Nine Cambridge Center > > Cambridge, MA 02142 > > > > > > On Mon, Jun 24, 2013 at 5:14 PM, James W. MacDonald > <jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu=""> > > <mailto:jmacdon at="" uw.edu="" <mailto:jmacdon="" at="" uw.edu="">>> wrote: > > > > Hi Brian, > > > > Sure. You can send it directly to me. > > > > Best, > > > > Jim > > > > > > > > > > On 6/24/2013 3:33 PM, Brian Abraham [guest] wrote: > > > > Hi team, > > > > I'm part of the lab that made everyone's microarray analysis > > more difficult by demanding everyone do ERCC spike-in > > normalization. Unfortunately, the primeviewcdf does not > > automatically contain the probeset IDs for ERCCs, > despite the > > probes being physically on the chip. We've worked with Affy > > to get a custom cdf made that contains the locations of the > > ERCC probes on the primeview chip. Would you be > interested in > > folding this into your code so that more people can benefit > > from it? > > > > -- output of sessionInfo(): > > > > sessionInfo() > > > > R version 3.0.1 (2013-05-16) > > Platform: x86_64-pc-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=C LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] parallel stats graphics grDevices utils > datasets > > methods > > [8] base > > > > other attached packages: > > [1] makecdfenv_1.36.0 affyio_1.28.0 affy_1.38.1 > > Biobase_2.20.0 > > [5] BiocGenerics_0.6.0 > > > > loaded via a namespace (and not attached): > > [1] BiocInstaller_1.10.2 preprocessCore_1.22.0 tools_3.0.1 > > [4] zlibbioc_1.6.0 > > > > -- > > Sent via the guest posting facility at bioconductor.org > <http: bioconductor.org=""> > > <http: bioconductor.org="">. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > <mailto:bioconductor at="" r-project.org=""> <mailto: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 > > > > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto: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
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