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Question: Installing Workflows for Oligonucleotide arrays
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4.2 years ago by
Guest User12k
Guest User12k wrote:
Is there a way to install workflows for microarray analysis on Bioconductor v2.14? or should i downgrade to bioconductor v2.13? > source("http://bioconductor.org/workflows.R") Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help Error: BiocInstaller:::BIOC_VERSION == "2.13" is not TRUE -- output of sessionInfo(): > sessionInfo() R version 3.1.0 (2014-04-10) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.14.2 loaded via a namespace (and not attached): [1] affyio_1.32.0 base64_1.1 Biobase_2.24.0 [4] BiocGenerics_0.10.0 Biostrings_2.32.0 bit_1.1-12 [7] codetools_0.2-8 digest_0.6.4 ellipse_0.3-8 [10] ff_2.2-13 foreach_1.4.2 GenomeInfoDb_1.0.2 [13] GenomicRanges_1.16.3 grid_3.1.0 illuminaio_0.6.0 [16] IRanges_1.22.8 iterators_1.0.7 lattice_0.20-29 [19] Matrix_1.1-3 matrixStats_0.10.0 mvtnorm_0.9-99992 [22] parallel_3.1.0 R.methodsS3_1.6.1 Rcpp_0.11.2 [25] RcppEigen_0.3.2.1.2 stats4_3.1.0 tools_3.1.0 [28] VGAM_0.9-4 XVector_0.4.0 zlibbioc_1.10.0 -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 4.2 years ago by Dan Tenenbaum ♦♦ 8.2k • written 4.2 years ago by Guest User12k
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gravatar for Dan Tenenbaum
4.2 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
----- Original Message ----- > From: "Rinaldy K [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, rinkz5 at gmail.com > Sent: Tuesday, June 10, 2014 2:40:14 AM > Subject: [BioC] Installing Workflows for Oligonucleotide arrays > > Is there a way to install workflows for microarray analysis on > Bioconductor v2.14? > > or should i downgrade to bioconductor v2.13? > This should be building for the latest release version (2.14). I'll look into it. Dan > > source("http://bioconductor.org/workflows.R") > Bioconductor version 2.14 (BiocInstaller > 1.14.2), ?biocLite for help > Error: BiocInstaller:::BIOC_VERSION == "2.13" is not TRUE > > -- output of sessionInfo(): > > > sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] affyio_1.32.0 base64_1.1 Biobase_2.24.0 > [4] BiocGenerics_0.10.0 Biostrings_2.32.0 bit_1.1-12 > [7] codetools_0.2-8 digest_0.6.4 ellipse_0.3-8 > [10] ff_2.2-13 foreach_1.4.2 GenomeInfoDb_1.0.2 > [13] GenomicRanges_1.16.3 grid_3.1.0 illuminaio_0.6.0 > [16] IRanges_1.22.8 iterators_1.0.7 lattice_0.20-29 > [19] Matrix_1.1-3 matrixStats_0.10.0 mvtnorm_0.9-99992 > [22] parallel_3.1.0 R.methodsS3_1.6.1 Rcpp_0.11.2 > [25] RcppEigen_0.3.2.1.2 stats4_3.1.0 tools_3.1.0 > [28] VGAM_0.9-4 XVector_0.4.0 zlibbioc_1.10.0 > > -- > 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 >
ADD COMMENTlink written 4.2 years ago by Dan Tenenbaum ♦♦ 8.2k
Thank you Dan for your help, i find it now changed to the latest version On Tue, Jun 10, 2014 at 10:33 PM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > > > ----- Original Message ----- > > From: "Rinaldy K [guest]" <guest@bioconductor.org> > > To: bioconductor@r-project.org, rinkz5@gmail.com > > Sent: Tuesday, June 10, 2014 2:40:14 AM > > Subject: [BioC] Installing Workflows for Oligonucleotide arrays > > > > Is there a way to install workflows for microarray analysis on > > Bioconductor v2.14? > > > > or should i downgrade to bioconductor v2.13? > > > > > This should be building for the latest release version (2.14). I'll look > into it. > > Dan > > > > > source("http://bioconductor.org/workflows.R") > > Bioconductor version 2.14 (BiocInstaller > > 1.14.2), ?biocLite for help > > Error: BiocInstaller:::BIOC_VERSION == "2.13" is not TRUE > > > > -- output of sessionInfo(): > > > > > sessionInfo() > > R version 3.1.0 (2014-04-10) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > > > locale: > > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United > > States.1252 > > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] BiocInstaller_1.14.2 > > > > loaded via a namespace (and not attached): > > [1] affyio_1.32.0 base64_1.1 Biobase_2.24.0 > > [4] BiocGenerics_0.10.0 Biostrings_2.32.0 bit_1.1-12 > > [7] codetools_0.2-8 digest_0.6.4 ellipse_0.3-8 > > [10] ff_2.2-13 foreach_1.4.2 GenomeInfoDb_1.0.2 > > [13] GenomicRanges_1.16.3 grid_3.1.0 illuminaio_0.6.0 > > [16] IRanges_1.22.8 iterators_1.0.7 lattice_0.20-29 > > [19] Matrix_1.1-3 matrixStats_0.10.0 mvtnorm_0.9-99992 > > [22] parallel_3.1.0 R.methodsS3_1.6.1 Rcpp_0.11.2 > > [25] RcppEigen_0.3.2.1.2 stats4_3.1.0 tools_3.1.0 > > [28] VGAM_0.9-4 XVector_0.4.0 zlibbioc_1.10.0 > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > 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 4.2 years ago by Rinaldy Kusuma10
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gravatar for James W. MacDonald
4.2 years ago by
United States
James W. MacDonald47k wrote:
Not sure what you are asking for here. Will you clarify please? Best, Jim On 6/10/2014 5:40 AM, Rinaldy K [guest] wrote: > Is there a way to install workflows for microarray analysis on Bioconductor v2.14? > > or should i downgrade to bioconductor v2.13? > >> source("http://bioconductor.org/workflows.R") > Bioconductor version 2.14 (BiocInstaller > 1.14.2), ?biocLite for help > Error: BiocInstaller:::BIOC_VERSION == "2.13" is not TRUE > > -- output of sessionInfo(): > >> sessionInfo() > R version 3.1.0 (2014-04-10) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.14.2 > > loaded via a namespace (and not attached): > [1] affyio_1.32.0 base64_1.1 Biobase_2.24.0 > [4] BiocGenerics_0.10.0 Biostrings_2.32.0 bit_1.1-12 > [7] codetools_0.2-8 digest_0.6.4 ellipse_0.3-8 > [10] ff_2.2-13 foreach_1.4.2 GenomeInfoDb_1.0.2 > [13] GenomicRanges_1.16.3 grid_3.1.0 illuminaio_0.6.0 > [16] IRanges_1.22.8 iterators_1.0.7 lattice_0.20-29 > [19] Matrix_1.1-3 matrixStats_0.10.0 mvtnorm_0.9-99992 > [22] parallel_3.1.0 R.methodsS3_1.6.1 Rcpp_0.11.2 > [25] RcppEigen_0.3.2.1.2 stats4_3.1.0 tools_3.1.0 > [28] VGAM_0.9-4 XVector_0.4.0 zlibbioc_1.10.0 > > -- > 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
ADD COMMENTlink written 4.2 years ago by James W. MacDonald47k
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