AnnotationDbi quesion please help
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David Lyon ▴ 340
@david-lyon-4016
Last seen 3.1 years ago
United States
How do I get to output the mapped keys for the all of the following "head(qcdata, 50)" eg : output the keys and values for "hugene10sttranscriptclusterENSEMBL has 20276 mapped keys (of 33297 keys)" and all the others Thanks for your help > qcdata=capture.output(hugene10sttranscriptcluster()) > head(qcdata, 50) [1] "Quality control information for hugene10sttranscriptcluster:" [2] "" [3] "" [4] "This package has the following mappings:" [5] "" [6] "hugene10sttranscriptclusterACCNUM has 32969 mapped keys (of 33297 keys)" [7] "hugene10sttranscriptclusterALIAS2PROBE has 74639 mapped keys (of 109070 keys)" [8] "hugene10sttranscriptclusterCHR has 21890 mapped keys (of 33297 keys)" [9] "hugene10sttranscriptclusterCHRLENGTHS has 25 mapped keys (of 25 keys)" [10] "hugene10sttranscriptclusterCHRLOC has 21134 mapped keys (of 33297 keys)" [11] "hugene10sttranscriptclusterCHRLOCEND has 21134 mapped keys (of 33297 keys)" [12] "hugene10sttranscriptclusterENSEMBL has 20276 mapped keys (of 33297 keys)" [13] "hugene10sttranscriptclusterENSEMBL2PROBE has 18678 mapped keys (of 19892 keys)" [14] "hugene10sttranscriptclusterENTREZID has 21891 mapped keys (of 33297 keys)" [15] "hugene10sttranscriptclusterENZYME has 2165 mapped keys (of 33297 keys)" [16] "hugene10sttranscriptclusterENZYME2PROBE has 900 mapped keys (of 901 keys)" [17] "hugene10sttranscriptclusterGENENAME has 21891 mapped keys (of 33297 keys)" [18] "hugene10sttranscriptclusterGO has 18441 mapped keys (of 33297 keys)" [19] "hugene10sttranscriptclusterGO2ALLPROBES has 11220 mapped keys (of 11236 keys)" [20] "hugene10sttranscriptclusterGO2PROBE has 8224 mapped keys (of 8245 keys)" [21] "hugene10sttranscriptclusterMAP has 21809 mapped keys (of 33297 keys)" [22] "hugene10sttranscriptclusterOMIM has 13697 mapped keys (of 33297 keys)" [23] "hugene10sttranscriptclusterPATH has 5447 mapped keys (of 33297 keys)" [24] "hugene10sttranscriptclusterPATH2PROBE has 220 mapped keys (of 220 keys)" [25] "hugene10sttranscriptclusterPFAM has 21342 mapped keys (of 33297 keys)" [26] "hugene10sttranscriptclusterPMID has 21451 mapped keys (of 33297 keys)" [27] "hugene10sttranscriptclusterPMID2PROBE has 244607 mapped keys (of 248847 keys)" [28] "hugene10sttranscriptclusterPROSITE has 21342 mapped keys (of 33297 keys)" [29] "hugene10sttranscriptclusterREFSEQ has 21721 mapped keys (of 33297 keys)" [30] "hugene10sttranscriptclusterSYMBOL has 21891 mapped keys (of 33297 keys)" [31] "hugene10sttranscriptclusterUNIGENE has 21474 mapped keys (of 33297 keys)" [32] "hugene10sttranscriptclusterUNIPROT has 20875 mapped keys (of 33297 keys)" [33] "" [34] "" [35] "Additional Information about this package:" [36] "" [37] "DB schema: HUMANCHIP_DB" [38] "DB schema version: 2.0" [39] "Organism: Homo sapiens" [40] "Date for NCBI data: 2009-Sep1" [41] "Date for GO data: 20090830" [42] "Date for KEGG data: 2009-Sep16" [43] "Date for Golden Path data: 2009-Jul5" [44] "Date for IPI data: 2009-Jul29" [45] "Date for Ensembl data: 2009-Jul14"
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@vincent-j-carey-jr-4
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is this a reasonable example of what you want? > toTable(hugene10sttranscriptclusterENSEMBL)[1:4,] probe_id ensembl_id 1 8039748 ENSG00000121410 2 7960947 ENSG00000175899 3 8144857 ENSG00000171428 4 8144866 ENSG00000156006 On Tue, May 18, 2010 at 7:21 PM, David Lyon <david_lyon3@yahoo.com> wrote: > How do I get to output the mapped keys for the all of the following > "head(qcdata, 50)" > > eg : output the keys and values for "hugene10sttranscriptclusterENSEMBL has > 20276 mapped keys (of 33297 keys)" > and all the others > > Thanks for your help > > > > > > qcdata=capture.output(hugene10sttranscriptcluster()) > > head(qcdata, 50) > [1] "Quality control information for hugene10sttranscriptcluster:" > [2] "" > [3] "" > [4] "This package has the following mappings:" > [5] "" > [6] "hugene10sttranscriptclusterACCNUM has 32969 mapped keys (of 33297 > keys)" > [7] "hugene10sttranscriptclusterALIAS2PROBE has 74639 mapped keys (of > 109070 keys)" > [8] "hugene10sttranscriptclusterCHR has 21890 mapped keys (of 33297 keys)" > [9] "hugene10sttranscriptclusterCHRLENGTHS has 25 mapped keys (of 25 > keys)" > [10] "hugene10sttranscriptclusterCHRLOC has 21134 mapped keys (of 33297 > keys)" > [11] "hugene10sttranscriptclusterCHRLOCEND has 21134 mapped keys (of 33297 > keys)" > [12] "hugene10sttranscriptclusterENSEMBL has 20276 mapped keys (of 33297 > keys)" > [13] "hugene10sttranscriptclusterENSEMBL2PROBE has 18678 mapped keys (of > 19892 keys)" > [14] "hugene10sttranscriptclusterENTREZID has 21891 mapped keys (of 33297 > keys)" > [15] "hugene10sttranscriptclusterENZYME has 2165 mapped keys (of 33297 > keys)" > [16] "hugene10sttranscriptclusterENZYME2PROBE has 900 mapped keys (of 901 > keys)" > [17] "hugene10sttranscriptclusterGENENAME has 21891 mapped keys (of 33297 > keys)" > [18] "hugene10sttranscriptclusterGO has 18441 mapped keys (of 33297 keys)" > [19] "hugene10sttranscriptclusterGO2ALLPROBES has 11220 mapped keys (of > 11236 keys)" > [20] "hugene10sttranscriptclusterGO2PROBE has 8224 mapped keys (of 8245 > keys)" > [21] "hugene10sttranscriptclusterMAP has 21809 mapped keys (of 33297 keys)" > [22] "hugene10sttranscriptclusterOMIM has 13697 mapped keys (of 33297 > keys)" > [23] "hugene10sttranscriptclusterPATH has 5447 mapped keys (of 33297 keys)" > [24] "hugene10sttranscriptclusterPATH2PROBE has 220 mapped keys (of 220 > keys)" > [25] "hugene10sttranscriptclusterPFAM has 21342 mapped keys (of 33297 > keys)" > [26] "hugene10sttranscriptclusterPMID has 21451 mapped keys (of 33297 > keys)" > [27] "hugene10sttranscriptclusterPMID2PROBE has 244607 mapped keys (of > 248847 keys)" > [28] "hugene10sttranscriptclusterPROSITE has 21342 mapped keys (of 33297 > keys)" > [29] "hugene10sttranscriptclusterREFSEQ has 21721 mapped keys (of 33297 > keys)" > [30] "hugene10sttranscriptclusterSYMBOL has 21891 mapped keys (of 33297 > keys)" > [31] "hugene10sttranscriptclusterUNIGENE has 21474 mapped keys (of 33297 > keys)" > [32] "hugene10sttranscriptclusterUNIPROT has 20875 mapped keys (of 33297 > keys)" > [33] "" > [34] "" > [35] "Additional Information about this package:" > [36] "" > [37] "DB schema: HUMANCHIP_DB" > [38] "DB schema version: 2.0" > [39] "Organism: Homo sapiens" > [40] "Date for NCBI data: 2009-Sep1" > [41] "Date for GO data: 20090830" > [42] "Date for KEGG data: 2009-Sep16" > [43] "Date for Golden Path data: 2009-Jul5" > [44] "Date for IPI data: 2009-Jul29" > [45] "Date for Ensembl data: 2009-Jul14" > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > 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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Thanks I should be able to script it from here does anyone know what the following results mean? > toTable(hugene10sttranscriptclusterCHRLOCEND) [1:7, ] probe_id end_location Chromosome 1 8039748 -63556677 19 2 7960947 -9159825 12 3 8144857 18125477 8 4 8144857 18125477 8 5 8144857 18125477 8 6 8144866 18303003 8 how can there be negative coordinates? ________________________________ From: Vincent Carey <stvjc@channing.harvard.edu> Cc: bioconductor@stat.math.ethz.ch Sent: Tue, May 18, 2010 7:46:50 PM Subject: Re: [BioC] AnnotationDbi quesion please help is this a reasonable example of what you want? > toTable(hugene10sttranscriptclusterENSEMBL)[1:4,] probe_id ensembl_id 1 8039748 ENSG00000121410 2 7960947 ENSG00000175899 3 8144857 ENSG00000171428 4 8144866 ENSG00000156006 >How do I get to output the mapped keys for the all of the following "head(qcdata, 50)" > >>eg : output the keys and values for "hugene10sttranscriptclusterENSEMBL has 20276 mapped keys (of 33297 keys)" >>and all the others > >>Thanks for your help > > > > >>> qcdata=capture.output(hugene10sttranscriptcluster()) >>> head(qcdata, 50) >> [1] "Quality control information for hugene10sttranscriptcluster:" >> [2] "" >> [3] "" >> [4] "This package has the following mappings:" >> [5] "" >> [6] "hugene10sttranscriptclusterACCNUM has 32969 mapped keys (of 33297 keys)" >> [7] "hugene10sttranscriptclusterALIAS2PROBE has 74639 mapped keys (of 109070 keys)" >> [8] "hugene10sttranscriptclusterCHR has 21890 mapped keys (of 33297 keys)" >> [9] "hugene10sttranscriptclusterCHRLENGTHS has 25 mapped keys (of 25 keys)" >>[10] "hugene10sttranscriptclusterCHRLOC has 21134 mapped keys (of 33297 keys)" >>[11] "hugene10sttranscriptclusterCHRLOCEND has 21134 mapped keys (of 33297 keys)" >>[12] "hugene10sttranscriptclusterENSEMBL has 20276 mapped keys (of 33297 keys)" >>[13] "hugene10sttranscriptclusterENSEMBL2PROBE has 18678 mapped keys (of 19892 keys)" >>[14] "hugene10sttranscriptclusterENTREZID has 21891 mapped keys (of 33297 keys)" >>[15] "hugene10sttranscriptclusterENZYME has 2165 mapped keys (of 33297 keys)" >>[16] "hugene10sttranscriptclusterENZYME2PROBE has 900 mapped keys (of 901 keys)" >>[17] "hugene10sttranscriptclusterGENENAME has 21891 mapped keys (of 33297 keys)" >>[18] "hugene10sttranscriptclusterGO has 18441 mapped keys (of 33297 keys)" >>[19] "hugene10sttranscriptclusterGO2ALLPROBES has 11220 mapped keys (of 11236 keys)" >>[20] "hugene10sttranscriptclusterGO2PROBE has 8224 mapped keys (of 8245 keys)" >>[21] "hugene10sttranscriptclusterMAP has 21809 mapped keys (of 33297 keys)" >>[22] "hugene10sttranscriptclusterOMIM has 13697 mapped keys (of 33297 keys)" >>[23] "hugene10sttranscriptclusterPATH has 5447 mapped keys (of 33297 keys)" >>[24] "hugene10sttranscriptclusterPATH2PROBE has 220 mapped keys (of 220 keys)" >>[25] "hugene10sttranscriptclusterPFAM has 21342 mapped keys (of 33297 keys)" >>[26] "hugene10sttranscriptclusterPMID has 21451 mapped keys (of 33297 keys)" >>[27] "hugene10sttranscriptclusterPMID2PROBE has 244607 mapped keys (of 248847 keys)" >>[28] "hugene10sttranscriptclusterPROSITE has 21342 mapped keys (of 33297 keys)" >>[29] "hugene10sttranscriptclusterREFSEQ has 21721 mapped keys (of 33297 keys)" >>[30] "hugene10sttranscriptclusterSYMBOL has 21891 mapped keys (of 33297 keys)" >>[31] "hugene10sttranscriptclusterUNIGENE has 21474 mapped keys (of 33297 keys)" >>[32] "hugene10sttranscriptclusterUNIPROT has 20875 mapped keys (of 33297 keys)" >>[33] "" >>[34] "" >>[35] "Additional Information about this package:" >>[36] "" >>[37] "DB schema: HUMANCHIP_DB" >>[38] "DB schema version: 2.0" >>[39] "Organism: Homo sapiens" >>[40] "Date for NCBI data: 2009-Sep1" >>[41] "Date for GO data: 20090830" >>[42] "Date for KEGG data: 2009-Sep16" >>[43] "Date for Golden Path data: 2009-Jul5" >>[44] "Date for IPI data: 2009-Jul29" >>[45] "Date for Ensembl data: 2009-Jul14" > >>_______________________________________________ >>Bioconductor mailing list >Bioconductor@stat.math.ethz.ch >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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OK it looks like its mapping on the opposite strand so its '-' ignore my last question thanks for your help vincent and everyone, I should be able to take it from here. ----- Original Message ---- From: David Lyon <david_lyon3@yahoo.com> To: Vincent Carey <stvjc at="" channing.harvard.edu=""> Cc: bioconductor at stat.math.ethz.ch Sent: Tue, May 18, 2010 8:35:42 PM Subject: Re: [BioC] AnnotationDbi quesion please help Thanks I should be able to script it from here does anyone know what the following results mean? > toTable(hugene10sttranscriptclusterCHRLOCEND) [1:7, ] probe_id end_location Chromosome 1 8039748 -63556677 19 2 7960947 -9159825 12 3 8144857 18125477 8 4 8144857 18125477 8 5 8144857 18125477 8 6 8144866 18303003 8 how can there be negative coordinates? ________________________________ From: Vincent Carey <stvjc@channing.harvard.edu> Cc: bioconductor at stat.math.ethz.ch Sent: Tue, May 18, 2010 7:46:50 PM Subject: Re: [BioC] AnnotationDbi quesion please help is this a reasonable example of what you want? > toTable(hugene10sttranscriptclusterENSEMBL)[1:4,] probe_id ensembl_id 1 8039748 ENSG00000121410 2 7960947 ENSG00000175899 3 8144857 ENSG00000171428 4 8144866 ENSG00000156006 >How do I get to output the mapped keys for the all of the following "head(qcdata, 50)" > >>eg : output the keys and values for "hugene10sttranscriptclusterENSEMBL has 20276 mapped keys (of 33297 keys)" >>and all the others > >>Thanks for your help > > > > >>> qcdata=capture.output(hugene10sttranscriptcluster()) >>> head(qcdata, 50) >> [1] "Quality control information for hugene10sttranscriptcluster:" >> [2] "" >> [3] "" >> [4] "This package has the following mappings:" >> [5] "" >> [6] "hugene10sttranscriptclusterACCNUM has 32969 mapped keys (of 33297 keys)" >> [7] "hugene10sttranscriptclusterALIAS2PROBE has 74639 mapped keys (of 109070 keys)" >> [8] "hugene10sttranscriptclusterCHR has 21890 mapped keys (of 33297 keys)" >> [9] "hugene10sttranscriptclusterCHRLENGTHS has 25 mapped keys (of 25 keys)" >>[10] "hugene10sttranscriptclusterCHRLOC has 21134 mapped keys (of 33297 keys)" >>[11] "hugene10sttranscriptclusterCHRLOCEND has 21134 mapped keys (of 33297 keys)" >>[12] "hugene10sttranscriptclusterENSEMBL has 20276 mapped keys (of 33297 keys)" >>[13] "hugene10sttranscriptclusterENSEMBL2PROBE has 18678 mapped keys (of 19892 keys)" >>[14] "hugene10sttranscriptclusterENTREZID has 21891 mapped keys (of 33297 keys)" >>[15] "hugene10sttranscriptclusterENZYME has 2165 mapped keys (of 33297 keys)" >>[16] "hugene10sttranscriptclusterENZYME2PROBE has 900 mapped keys (of 901 keys)" >>[17] "hugene10sttranscriptclusterGENENAME has 21891 mapped keys (of 33297 keys)" >>[18] "hugene10sttranscriptclusterGO has 18441 mapped keys (of 33297 keys)" >>[19] "hugene10sttranscriptclusterGO2ALLPROBES has 11220 mapped keys (of 11236 keys)" >>[20] "hugene10sttranscriptclusterGO2PROBE has 8224 mapped keys (of 8245 keys)" >>[21] "hugene10sttranscriptclusterMAP has 21809 mapped keys (of 33297 keys)" >>[22] "hugene10sttranscriptclusterOMIM has 13697 mapped keys (of 33297 keys)" >>[23] "hugene10sttranscriptclusterPATH has 5447 mapped keys (of 33297 keys)" >>[24] "hugene10sttranscriptclusterPATH2PROBE has 220 mapped keys (of 220 keys)" >>[25] "hugene10sttranscriptclusterPFAM has 21342 mapped keys (of 33297 keys)" >>[26] "hugene10sttranscriptclusterPMID has 21451 mapped keys (of 33297 keys)" >>[27] "hugene10sttranscriptclusterPMID2PROBE has 244607 mapped keys (of 248847 keys)" >>[28] "hugene10sttranscriptclusterPROSITE has 21342 mapped keys (of 33297 keys)" >>[29] "hugene10sttranscriptclusterREFSEQ has 21721 mapped keys (of 33297 keys)" >>[30] "hugene10sttranscriptclusterSYMBOL has 21891 mapped keys (of 33297 keys)" >>[31] "hugene10sttranscriptclusterUNIGENE has 21474 mapped keys (of 33297 keys)" >>[32] "hugene10sttranscriptclusterUNIPROT has 20875 mapped keys (of 33297 keys)" >>[33] "" >>[34] "" >>[35] "Additional Information about this package:" >>[36] "" >>[37] "DB schema: HUMANCHIP_DB" >>[38] "DB schema version: 2.0" >>[39] "Organism: Homo sapiens" >>[40] "Date for NCBI data: 2009-Sep1" >>[41] "Date for GO data: 20090830" >>[42] "Date for KEGG data: 2009-Sep16" >>[43] "Date for Golden Path data: 2009-Jul5" >>[44] "Date for IPI data: 2009-Jul29" >>[45] "Date for Ensembl data: 2009-Jul14" > >>_______________________________________________ >>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 > [[alternative HTML version deleted]] _______________________________________________ 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
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I can download and install * DONE (hugene10sttranscriptcluster.db) but have problems with hugene11sttranscriptcluster.db: package ?hugene11sttranscriptcluster.db? is not available Does anyone else have this problem or is there something silly that I am doing? thanks
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On 05/18/2010 06:15 PM, David Lyon wrote: > I can download and install > * DONE (hugene10sttranscriptcluster.db) > > but have problems with hugene11sttranscriptcluster.db: > package ?hugene11sttranscriptcluster.db? is not available > > Does anyone else have this problem or is there something silly that I am doing? Hi David -- source("http://bioconductor.org/biocLite.R") biocLite("hugene11sttranscriptcluster.db") Works for me. What is your sessionInfo() ? What does 'download and install' mean to you? Martin > sessionInfo() R version 2.11.0 Patched (2010-05-01 r51886) x86_64-unknown-linux-gnu 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=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.11.0 > > thanks > > > > > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Thanks for your help Martin sessioninfo as below: > sessionInfo() R version 2.10.1 (2009-12-14) i486-pc-linux-gnu locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.10.1 ----- Original Message ---- From: Martin Morgan <mtmorgan@fhcrc.org> To: David Lyon <david_lyon3 at="" yahoo.com=""> Cc: bioconductor at stat.math.ethz.ch Sent: Tue, May 18, 2010 10:22:22 PM Subject: Re: [BioC] package ?hugene11sttranscriptcluster.db? is not available On 05/18/2010 06:15 PM, David Lyon wrote: > I can download and install > * DONE (hugene10sttranscriptcluster.db) > > but have problems with hugene11sttranscriptcluster.db: > package ?hugene11sttranscriptcluster.db? is not available > > Does anyone else have this problem or is there something silly that I am doing? Hi David -- source("http://bioconductor.org/biocLite.R") biocLite("hugene11sttranscriptcluster.db") Works for me. What is your sessionInfo() ? What does 'download and install' mean to you? Martin > sessionInfo() R version 2.11.0 Patched (2010-05-01 r51886) x86_64-unknown-linux-gnu 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=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.11.0 > > thanks > > > > > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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On 05/18/2010 07:26 PM, David Lyon wrote: > Thanks for your help Martin > > sessioninfo as below: > > >> sessionInfo() > R version 2.10.1 (2009-12-14) > i486-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.10.1 I think because it is not available for the R-2.10 series, perhaps because the chip itself was released just immediately before the corresponding Bioconductor release (I'm guessing about the explicit reason, based on dates in the NetAffx annotation files). I found this out with the relatively non-intuitive commands source('http://bioconductor.org/biocLite.R') pkgs = available.packages(contrib.url(biocinstallRepos())) rownames(pkgs)[grepl("hugene1[01]stt", rownames(pkgs))] and similarly non-intuitive navigation from bioconductor.org through 'Software' on the left, 'BiocViews' at the top, 'AnnotationData', then editing the URL to read '2.5' rather than 'release'. The solution is to update to R-2.11. Also I don't know what you're doing with this, but I'll mention oligo and the pd.hugene.1.1.st.v1 package (again with R-2.11). Martin > > > > > > > ----- Original Message ---- > From: Martin Morgan <mtmorgan at="" fhcrc.org=""> > To: David Lyon <david_lyon3 at="" yahoo.com=""> > Cc: bioconductor at stat.math.ethz.ch > Sent: Tue, May 18, 2010 10:22:22 PM > Subject: Re: [BioC] package ?hugene11sttranscriptcluster.db? is not available > > On 05/18/2010 06:15 PM, David Lyon wrote: >> I can download and install >> * DONE (hugene10sttranscriptcluster.db) >> >> but have problems with hugene11sttranscriptcluster.db: >> package ?hugene11sttranscriptcluster.db? is not available >> >> Does anyone else have this problem or is there something silly that I am doing? > > Hi David -- > > source("http://bioconductor.org/biocLite.R") > biocLite("hugene11sttranscriptcluster.db") > > Works for me. > > What is your sessionInfo() ? > > What does 'download and install' mean to you? > > Martin > >> sessionInfo() > R version 2.11.0 Patched (2010-05-01 r51886) > x86_64-unknown-linux-gnu > > 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=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.11.0 > >> >> thanks >> >> >> >> >> >> _______________________________________________ >> 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 > > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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Hi Martin Thank you very much it appears that corrected the problem "The solution is to update to R-2.11." For those who are using ubuntu and in the same position and need to upgrade: http://cran.r-project.org/bin/linux/ubuntu/ Also thanks for the tip about pd.hugene.1.1.st.v1 package ----- Original Message ---- From: Martin Morgan <mtmorgan@fhcrc.org> To: David Lyon <david_lyon3 at="" yahoo.com=""> Cc: bioconductor at stat.math.ethz.ch Sent: Tue, May 18, 2010 10:54:59 PM Subject: Re: [BioC] package ?hugene11sttranscriptcluster.db? is not available On 05/18/2010 07:26 PM, David Lyon wrote: > Thanks for your help Martin > > sessioninfo as below: > > >> sessionInfo() > R version 2.10.1 (2009-12-14) > i486-pc-linux-gnu > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.10.1 I think because it is not available for the R-2.10 series, perhaps because the chip itself was released just immediately before the corresponding Bioconductor release (I'm guessing about the explicit reason, based on dates in the NetAffx annotation files). I found this out with the relatively non-intuitive commands source('http://bioconductor.org/biocLite.R') pkgs = available.packages(contrib.url(biocinstallRepos())) rownames(pkgs)[grepl("hugene1[01]stt", rownames(pkgs))] and similarly non-intuitive navigation from bioconductor.org through 'Software' on the left, 'BiocViews' at the top, 'AnnotationData', then editing the URL to read '2.5' rather than 'release'. The solution is to update to R-2.11. Also I don't know what you're doing with this, but I'll mention oligo and the pd.hugene.1.1.st.v1 package (again with R-2.11). Martin > > > > > > > ----- Original Message ---- > From: Martin Morgan <mtmorgan at="" fhcrc.org=""> > To: David Lyon <david_lyon3 at="" yahoo.com=""> > Cc: bioconductor at stat.math.ethz.ch > Sent: Tue, May 18, 2010 10:22:22 PM > Subject: Re: [BioC] package ?hugene11sttranscriptcluster.db? is not available > > On 05/18/2010 06:15 PM, David Lyon wrote: >> I can download and install >> * DONE (hugene10sttranscriptcluster.db) >> >> but have problems with hugene11sttranscriptcluster.db: >> package ?hugene11sttranscriptcluster.db? is not available >> >> Does anyone else have this problem or is there something silly that I am doing? > > Hi David -- > > source("http://bioconductor.org/biocLite.R") > biocLite("hugene11sttranscriptcluster.db") > > Works for me. > > What is your sessionInfo() ? > > What does 'download and install' mean to you? > > Martin > >> sessionInfo() > R version 2.11.0 Patched (2010-05-01 r51886) > x86_64-unknown-linux-gnu > > 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=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > [1] tools_2.11.0 > >> >> thanks >> >> >> >> >> >> _______________________________________________ >> 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 > > -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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