ecoli2.db
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@clementine-dressaire-4294
Last seen 10.3 years ago
Dear BioC members, I was looking for a ecoli2.db annotation file but could not find it in Bioconductor (or elsewhere). From previous posts I saw that some people have already asked for this and were considering creating one. Can anyone tell me if such a work is in process or still a project? If not I will try to create my own. Is SQLForge package the most appropriated for this purpose taking into account that I only have Affymetrix annotation file? With adavanced thanks for your help, Cl?mentine. -- Cl?mentine Dressaire Post-doctoral research fellow Control of gene expression lab (Pr. C?cilia Arraiano) ITQB - Instituto de Tecnologia Qu?mica e Biol?gica Apartado 127, Av. da Rep?blica 2780-157 Oeiras Portugal +351 214469562
Annotation PROcess Annotation PROcess • 1.6k views
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Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 8.4 years ago
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Hi Cl?mentine, There is both an org package for E coli and also a .db0 package. The existence of the .db0 package means that you can use the vignette titled "SQLForge: An easy way to create a new annotation package with a standard database schema." in the AnnotationDbi package to generate a chip package for E coli. You can find it here: http://www.bioconductor.org/help/bioc- views/devel/bioc/html/AnnotationDbi.html But since this is an affymetrix package, I just went ahead and added an ecoli2 chip package to the repository for you. Be forewarned though, that while this platform has probes to measure 4 different strains of E coli, I can only used the annotations for the popular K12 strain to make this package. If you want to get additional annotations for the other strains, you might be able to get one more in a separate package (if one of the strains is the Sakai strain), but after that things become much more difficult to support... Be sure to let us know whether or not this meets your needs. The annotations are always a work in progress and we always benefit from feedback to indicate what people are using, and what things might be missing. Marc On 10/14/2010 02:43 AM, Cl?mentine Dressaire wrote: > Dear BioC members, > > > > I was looking for a ecoli2.db annotation file but could not find it in > > Bioconductor (or elsewhere). From previous posts I saw that some people > > have already asked for this and were considering creating one. Can anyone > > tell me if such a work is in process or still a project? If not I will try > > to create my own. Is SQLForge package the most appropriated for this > > purpose taking into account that I only have Affymetrix annotation file? > > > > With adavanced thanks for your help, > > > > Cl?mentine. > > > >
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Dear Marc, Since I work with the MG1655 (K12) strain it should be enough for me to have only annotations for this one. Nevertheless I cannot find the ecoli2 chip package you added neither in Bioconductor website nor using AnnotationDbi package in R. Does it mean that it has not been released yeat or that I have to use the ecoliK12.db0? Unlesss I am not looking in the right place? Thanks for your help, be sure it is usefull! Cl?mentine On Thu, 14 Oct 2010 13:50:43 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Cl?mentine, > > There is both an org package for E coli and also a .db0 package. The > existence of the .db0 package means that you can use the vignette titled > "SQLForge: An easy way to create a new annotation package with a > standard database schema." in the AnnotationDbi package to generate a > chip package for E coli. You can find it here: > > http://www.bioconductor.org/help/bioc- views/devel/bioc/html/AnnotationDbi.html > > But since this is an affymetrix package, I just went ahead and added an > ecoli2 chip package to the repository for you. > > Be forewarned though, that while this platform has probes to measure 4 > different strains of E coli, I can only used the annotations for the > popular K12 strain to make this package. If you want to get additional > annotations for the other strains, you might be able to get one more in > a separate package (if one of the strains is the Sakai strain), but > after that things become much more difficult to support... Be sure to > let us know whether or not this meets your needs. The annotations are > always a work in progress and we always benefit from feedback to > indicate what people are using, and what things might be missing. > > > Marc > > > > > On 10/14/2010 02:43 AM, Cl?mentine Dressaire wrote: >> Dear BioC members, >> >> >> >> I was looking for a ecoli2.db annotation file but could not find it in >> >> Bioconductor (or elsewhere). From previous posts I saw that some people >> >> have already asked for this and were considering creating one. Can anyone >> >> tell me if such a work is in process or still a project? If not I will >> try >> >> to create my own. Is SQLForge package the most appropriated for this >> >> purpose taking into account that I only have Affymetrix annotation file? >> >> >> >> With adavanced thanks for your help, >> >> >> >> Cl?mentine. >> >> >> >> > > _______________________________________________ > 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 -- Cl?mentine Dressaire Post-doctoral research fellow Control of gene expression lab ITQB - Instituto de Tecnologia Qu?mica e Biol?gica Apartado 127, Av. da Rep?blica 2780-157 Oeiras Portugal +351 214469562
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Hi Cl?mentine, That is probably because I have dropped it into the devel branch. I will become the release branch next week. I think that most people are like you and will only care about the K12 strain. But I have to post a disclaimer (and one is planned for when the package loads), simply because the probes on this platform were planned for detecting 4 strains, and we only have annotation for the popular one here. Marc On 10/15/2010 02:10 AM, Cl?mentine Dressaire wrote: > Dear Marc, > > Since I work with the MG1655 (K12) strain it should be enough for me to > have only annotations for this one. > Nevertheless I cannot find the ecoli2 chip package you added neither in > Bioconductor website nor using AnnotationDbi package in R. Does it mean > that it has not been released yeat or that I have to use the ecoliK12.db0? > Unlesss I am not looking in the right place? > > Thanks for your help, be sure it is usefull! > > Cl?mentine > > > On Thu, 14 Oct 2010 13:50:43 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> > wrote: > >> Hi Cl?mentine, >> >> There is both an org package for E coli and also a .db0 package. The >> existence of the .db0 package means that you can use the vignette titled >> "SQLForge: An easy way to create a new annotation package with a >> standard database schema." in the AnnotationDbi package to generate a >> chip package for E coli. You can find it here: >> >> >> > http://www.bioconductor.org/help/bioc- views/devel/bioc/html/AnnotationDbi.html > >> But since this is an affymetrix package, I just went ahead and added an >> ecoli2 chip package to the repository for you. >> >> Be forewarned though, that while this platform has probes to measure 4 >> different strains of E coli, I can only used the annotations for the >> popular K12 strain to make this package. If you want to get additional >> annotations for the other strains, you might be able to get one more in >> a separate package (if one of the strains is the Sakai strain), but >> after that things become much more difficult to support... Be sure to >> let us know whether or not this meets your needs. The annotations are >> always a work in progress and we always benefit from feedback to >> indicate what people are using, and what things might be missing. >> >> >> Marc >> >> >> >> >> On 10/14/2010 02:43 AM, Cl?mentine Dressaire wrote: >> >>> Dear BioC members, >>> >>> >>> >>> I was looking for a ecoli2.db annotation file but could not find it in >>> >>> Bioconductor (or elsewhere). From previous posts I saw that some people >>> >>> have already asked for this and were considering creating one. Can >>> > anyone > >>> tell me if such a work is in process or still a project? If not I will >>> try >>> >>> to create my own. Is SQLForge package the most appropriated for this >>> >>> purpose taking into account that I only have Affymetrix annotation >>> > file? > >>> >>> >>> With adavanced thanks for your help, >>> >>> >>> >>> Cl?mentine. >>> >>> >>> >>> >>> >> _______________________________________________ >> 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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Hello Marc, After making sure that ecoli2.db was available in Bioconductor 2.7 released I tried several times today to install the package as follows and got an error message about ecoli2.db availability: source("http://bioconductor.org/biocLite.R") BioC_mirror = http://www.bioconductor.org Change using chooseBioCmirror(). > biocLite("ecoli2.db") Using R version 2.12.0, biocinstall version 2.7.4. Installing Bioconductor version 2.7 packages: [1] "ecoli2.db" Please wait... Message d'avis : In getDependencies(pkgs, dependencies, available, lib) : package ?ecoli2.db? is not available Could you please tell me if I am doing something wrong of if this come from a Bioconductor problem that you can fix? Thanks for your precious help, Cl?mentine On Fri, 15 Oct 2010 09:09:40 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Cl?mentine, > > That is probably because I have dropped it into the devel branch. I > will become the release branch next week. I think that most people are > like you and will only care about the K12 strain. But I have to post a > disclaimer (and one is planned for when the package loads), simply > because the probes on this platform were planned for detecting 4 > strains, and we only have annotation for the popular one here. > > > Marc > > > > On 10/15/2010 02:10 AM, Cl?mentine Dressaire wrote: >> Dear Marc, >> >> Since I work with the MG1655 (K12) strain it should be enough for me to >> have only annotations for this one. >> Nevertheless I cannot find the ecoli2 chip package you added neither in >> Bioconductor website nor using AnnotationDbi package in R. Does it mean >> that it has not been released yeat or that I have to use the >> ecoliK12.db0? >> Unlesss I am not looking in the right place? >> >> Thanks for your help, be sure it is usefull! >> >> Cl?mentine >> >> >> On Thu, 14 Oct 2010 13:50:43 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> >> wrote: >> >>> Hi Cl?mentine, >>> >>> There is both an org package for E coli and also a .db0 package. The >>> existence of the .db0 package means that you can use the vignette titled >>> "SQLForge: An easy way to create a new annotation package with a >>> standard database schema." in the AnnotationDbi package to generate a >>> chip package for E coli. You can find it here: >>> >>> >>> >> http://www.bioconductor.org/help/bioc- views/devel/bioc/html/AnnotationDbi.html >> >>> But since this is an affymetrix package, I just went ahead and added an >>> ecoli2 chip package to the repository for you. >>> >>> Be forewarned though, that while this platform has probes to measure 4 >>> different strains of E coli, I can only used the annotations for the >>> popular K12 strain to make this package. If you want to get additional >>> annotations for the other strains, you might be able to get one more in >>> a separate package (if one of the strains is the Sakai strain), but >>> after that things become much more difficult to support... Be sure to >>> let us know whether or not this meets your needs. The annotations are >>> always a work in progress and we always benefit from feedback to >>> indicate what people are using, and what things might be missing. >>> >>> >>> Marc >>> >>> >>> >>> >>> On 10/14/2010 02:43 AM, Cl?mentine Dressaire wrote: >>> >>>> Dear BioC members, >>>> >>>> >>>> >>>> I was looking for a ecoli2.db annotation file but could not find it in >>>> >>>> Bioconductor (or elsewhere). From previous posts I saw that some people >>>> >>>> have already asked for this and were considering creating one. Can >>>> >> anyone >> >>>> tell me if such a work is in process or still a project? If not I will >>>> try >>>> >>>> to create my own. Is SQLForge package the most appropriated for this >>>> >>>> purpose taking into account that I only have Affymetrix annotation >>>> >> file? >> >>>> >>>> >>>> With adavanced thanks for your help, >>>> >>>> >>>> >>>> Cl?mentine. >>>> >>>> >>>> >>>> >>>> >>> _______________________________________________ >>> 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 >>> >> -- Cl?mentine Dressaire Post-doctoral research fellow Control of gene expression lab ITQB - Instituto de Tecnologia Qu?mica e Biol?gica Apartado 127, Av. da Rep?blica 2780-157 Oeiras Portugal +351 214469562
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Hi Cl?mentine, I am still building the Mac binaries for this, so the issue might be caused by the fact that (so far) only the tarball is available. It would help me if you gave the output of sessionInfo() so that I know what version of things you are even using. If you are using Mac or Windows and don't want to wait till later in the day when I get those binaries built, you can try this (which should work): biocLite("ecoli2.db", type="source") And if that doesn't help you, then please use sessionInfo() and get back to me. Marc On 10/19/2010 07:21 AM, Cl?mentine Dressaire wrote: > Hello Marc, > > After making sure that ecoli2.db was available in Bioconductor 2.7 > released I tried several times today to install the package as follows and > got an error message > about ecoli2.db availability: > > source("http://bioconductor.org/biocLite.R") > BioC_mirror = http://www.bioconductor.org > Change using chooseBioCmirror(). > >> biocLite("ecoli2.db") >> > Using R version 2.12.0, biocinstall version 2.7.4. > Installing Bioconductor version 2.7 packages: > [1] "ecoli2.db" > Please wait... > > Message d'avis : > In getDependencies(pkgs, dependencies, available, lib) : > package ?ecoli2.db? is not available > > Could you please tell me if I am doing something wrong of if this come > from a Bioconductor problem that you can fix? > > Thanks for your precious help, > > Cl?mentine > > > > > On Fri, 15 Oct 2010 09:09:40 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> > wrote: > >> Hi Cl?mentine, >> >> That is probably because I have dropped it into the devel branch. I >> will become the release branch next week. I think that most people are >> like you and will only care about the K12 strain. But I have to post a >> disclaimer (and one is planned for when the package loads), simply >> because the probes on this platform were planned for detecting 4 >> strains, and we only have annotation for the popular one here. >> >> >> Marc >> >> >> >> On 10/15/2010 02:10 AM, Cl?mentine Dressaire wrote: >> >>> Dear Marc, >>> >>> Since I work with the MG1655 (K12) strain it should be enough for me to >>> have only annotations for this one. >>> Nevertheless I cannot find the ecoli2 chip package you added neither in >>> Bioconductor website nor using AnnotationDbi package in R. Does it mean >>> that it has not been released yeat or that I have to use the >>> ecoliK12.db0? >>> Unlesss I am not looking in the right place? >>> >>> Thanks for your help, be sure it is usefull! >>> >>> Cl?mentine >>> >>> >>> On Thu, 14 Oct 2010 13:50:43 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> >>> wrote: >>> >>> >>>> Hi Cl?mentine, >>>> >>>> There is both an org package for E coli and also a .db0 package. The >>>> existence of the .db0 package means that you can use the vignette >>>> > titled > >>>> "SQLForge: An easy way to create a new annotation package with a >>>> standard database schema." in the AnnotationDbi package to generate a >>>> chip package for E coli. You can find it here: >>>> >>>> >>>> >>>> >>> > http://www.bioconductor.org/help/bioc- views/devel/bioc/html/AnnotationDbi.html > >>> >>> >>>> But since this is an affymetrix package, I just went ahead and added >>>> > an > >>>> ecoli2 chip package to the repository for you. >>>> >>>> Be forewarned though, that while this platform has probes to measure 4 >>>> different strains of E coli, I can only used the annotations for the >>>> popular K12 strain to make this package. If you want to get >>>> > additional > >>>> annotations for the other strains, you might be able to get one more >>>> > in > >>>> a separate package (if one of the strains is the Sakai strain), but >>>> after that things become much more difficult to support... Be sure to >>>> let us know whether or not this meets your needs. The annotations are >>>> always a work in progress and we always benefit from feedback to >>>> indicate what people are using, and what things might be missing. >>>> >>>> >>>> Marc >>>> >>>> >>>> >>>> >>>> On 10/14/2010 02:43 AM, Cl?mentine Dressaire wrote: >>>> >>>> >>>>> Dear BioC members, >>>>> >>>>> >>>>> >>>>> I was looking for a ecoli2.db annotation file but could not find it >>>>> > in > >>>>> Bioconductor (or elsewhere). From previous posts I saw that some >>>>> > people > >>>>> have already asked for this and were considering creating one. Can >>>>> >>>>> >>> anyone >>> >>> >>>>> tell me if such a work is in process or still a project? If not I >>>>> > will > >>>>> try >>>>> >>>>> to create my own. Is SQLForge package the most appropriated for this >>>>> >>>>> purpose taking into account that I only have Affymetrix annotation >>>>> >>>>> >>> file? >>> >>> >>>>> >>>>> With adavanced thanks for your help, >>>>> >>>>> >>>>> >>>>> Cl?mentine. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> _______________________________________________ >>>> 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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Hello again, Here is the outpout of my sessionInfo(): > sessionInfo() R version 2.12.0 (2010-10-15) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ecoli2cdf_2.6.0 simpleaffy_2.26.0 gcrma_2.22.0 [4] genefilter_1.32.0 annotate_1.28.0 biomaRt_2.6.0 [7] GOstats_2.16.0 graph_1.28.0 Category_2.16.0 [10] annaffy_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 [13] RSQLite_0.9-2 DBI_0.2-5 AnnotationDbi_1.12.0 [16] lattice_0.19-13 affy_1.28.0 Biobase_2.10.0 [19] limma_3.6.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 Biostrings_2.18.0 grid_2.12.0 [4] GSEABase_1.12.0 IRanges_1.8.0 preprocessCore_1.12.0 [7] RBGL_1.25.1 RCurl_1.4-4.1 splines_2.12.0 [10] survival_2.35-8 tools_2.12.0 XML_3.2-0.1 [13] xtable_1.5-6 I hope it will help you. I do not have time to try the trick today but thanks anyway, Cl?mentine On Tue, 19 Oct 2010 10:50:40 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Cl?mentine, > > I am still building the Mac binaries for this, so the issue might be > caused by the fact that (so far) only the tarball is available. It > would help me if you gave the output of sessionInfo() so that I know > what version of things you are even using. If you are using Mac or > Windows and don't want to wait till later in the day when I get those > binaries built, you can try this (which should work): > > biocLite("ecoli2.db", type="source") > > And if that doesn't help you, then please use sessionInfo() and get back > to me. > > > Marc > > > > On 10/19/2010 07:21 AM, Cl?mentine Dressaire wrote: >> Hello Marc, >> >> After making sure that ecoli2.db was available in Bioconductor 2.7 >> released I tried several times today to install the package as follows >> and >> got an error message >> about ecoli2.db availability: >> >> source("http://bioconductor.org/biocLite.R") >> BioC_mirror = http://www.bioconductor.org >> Change using chooseBioCmirror(). >> >>> biocLite("ecoli2.db") >>> >> Using R version 2.12.0, biocinstall version 2.7.4. >> Installing Bioconductor version 2.7 packages: >> [1] "ecoli2.db" >> Please wait... >> >> Message d'avis : >> In getDependencies(pkgs, dependencies, available, lib) : >> package ?ecoli2.db? is not available >> >> Could you please tell me if I am doing something wrong of if this come >> from a Bioconductor problem that you can fix? >> >> Thanks for your precious help, >> >> Cl?mentine >> >> >> >> >> On Fri, 15 Oct 2010 09:09:40 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> >> wrote: >> >>> Hi Cl?mentine, >>> >>> That is probably because I have dropped it into the devel branch. I >>> will become the release branch next week. I think that most people are >>> like you and will only care about the K12 strain. But I have to post a >>> disclaimer (and one is planned for when the package loads), simply >>> because the probes on this platform were planned for detecting 4 >>> strains, and we only have annotation for the popular one here. >>> >>> >>> Marc >>> >>> >>> >>> On 10/15/2010 02:10 AM, Cl?mentine Dressaire wrote: >>> >>>> Dear Marc, >>>> >>>> Since I work with the MG1655 (K12) strain it should be enough for me to >>>> have only annotations for this one. >>>> Nevertheless I cannot find the ecoli2 chip package you added neither in >>>> Bioconductor website nor using AnnotationDbi package in R. Does it mean >>>> that it has not been released yeat or that I have to use the >>>> ecoliK12.db0? >>>> Unlesss I am not looking in the right place? >>>> >>>> Thanks for your help, be sure it is usefull! >>>> >>>> Cl?mentine >>>> >>>> >>>> On Thu, 14 Oct 2010 13:50:43 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> >>>> wrote: >>>> >>>> >>>>> Hi Cl?mentine, >>>>> >>>>> There is both an org package for E coli and also a .db0 package. The >>>>> existence of the .db0 package means that you can use the vignette >>>>> >> titled >> >>>>> "SQLForge: An easy way to create a new annotation package with a >>>>> standard database schema." in the AnnotationDbi package to generate a >>>>> chip package for E coli. You can find it here: >>>>> >>>>> >>>>> >>>>> >>>> >> http://www.bioconductor.org/help/bioc- views/devel/bioc/html/AnnotationDbi.html >> >>>> >>>> >>>>> But since this is an affymetrix package, I just went ahead and added >>>>> >> an >> >>>>> ecoli2 chip package to the repository for you. >>>>> >>>>> Be forewarned though, that while this platform has probes to measure 4 >>>>> different strains of E coli, I can only used the annotations for the >>>>> popular K12 strain to make this package. If you want to get >>>>> >> additional >> >>>>> annotations for the other strains, you might be able to get one more >>>>> >> in >> >>>>> a separate package (if one of the strains is the Sakai strain), but >>>>> after that things become much more difficult to support... Be sure to >>>>> let us know whether or not this meets your needs. The annotations are >>>>> always a work in progress and we always benefit from feedback to >>>>> indicate what people are using, and what things might be missing. >>>>> >>>>> >>>>> Marc >>>>> >>>>> >>>>> >>>>> >>>>> On 10/14/2010 02:43 AM, Cl?mentine Dressaire wrote: >>>>> >>>>> >>>>>> Dear BioC members, >>>>>> >>>>>> >>>>>> >>>>>> I was looking for a ecoli2.db annotation file but could not find it >>>>>> >> in >> >>>>>> Bioconductor (or elsewhere). From previous posts I saw that some >>>>>> >> people >> >>>>>> have already asked for this and were considering creating one. Can >>>>>> >>>>>> >>>> anyone >>>> >>>> >>>>>> tell me if such a work is in process or still a project? If not I >>>>>> >> will >> >>>>>> try >>>>>> >>>>>> to create my own. Is SQLForge package the most appropriated for this >>>>>> >>>>>> purpose taking into account that I only have Affymetrix annotation >>>>>> >>>>>> >>>> file? >>>> >>>> >>>>>> >>>>>> With adavanced thanks for your help, >>>>>> >>>>>> >>>>>> >>>>>> Cl?mentine. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> >>>> >> -- Cl?mentine Dressaire Post-doctoral research fellow Control of gene expression lab ITQB - Instituto de Tecnologia Qu?mica e Biol?gica Apartado 127, Av. da Rep?blica 2780-157 Oeiras Portugal +351 214469562
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Hi Cl?mentine, The windows binary for ecoli2.db should be available now. Marc On 10/19/2010 11:03 AM, Cl?mentine Dressaire wrote: > Hello again, > > Here is the outpout of my sessionInfo(): > > >> sessionInfo() >> > R version 2.12.0 (2010-10-15) > Platform: i386-pc-mingw32/i386 (32-bit) > > locale: > [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 > [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C > [5] LC_TIME=French_France.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] ecoli2cdf_2.6.0 simpleaffy_2.26.0 gcrma_2.22.0 > [4] genefilter_1.32.0 annotate_1.28.0 biomaRt_2.6.0 > [7] GOstats_2.16.0 graph_1.28.0 Category_2.16.0 > [10] annaffy_1.22.0 KEGG.db_2.4.5 GO.db_2.4.5 > [13] RSQLite_0.9-2 DBI_0.2-5 AnnotationDbi_1.12.0 > [16] lattice_0.19-13 affy_1.28.0 Biobase_2.10.0 > [19] limma_3.6.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 Biostrings_2.18.0 grid_2.12.0 > [4] GSEABase_1.12.0 IRanges_1.8.0 preprocessCore_1.12.0 > [7] RBGL_1.25.1 RCurl_1.4-4.1 splines_2.12.0 > [10] survival_2.35-8 tools_2.12.0 XML_3.2-0.1 > [13] xtable_1.5-6 > > > I hope it will help you. I do not have time to try the trick today but > thanks anyway, > > Cl?mentine > > On Tue, 19 Oct 2010 10:50:40 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> > wrote: > >> Hi Cl?mentine, >> >> I am still building the Mac binaries for this, so the issue might be >> caused by the fact that (so far) only the tarball is available. It >> would help me if you gave the output of sessionInfo() so that I know >> what version of things you are even using. If you are using Mac or >> Windows and don't want to wait till later in the day when I get those >> binaries built, you can try this (which should work): >> >> biocLite("ecoli2.db", type="source") >> >> And if that doesn't help you, then please use sessionInfo() and get back >> to me. >> >> >> Marc >> >> >> >> On 10/19/2010 07:21 AM, Cl?mentine Dressaire wrote: >> >>> Hello Marc, >>> >>> After making sure that ecoli2.db was available in Bioconductor 2.7 >>> released I tried several times today to install the package as follows >>> and >>> got an error message >>> about ecoli2.db availability: >>> >>> source("http://bioconductor.org/biocLite.R") >>> BioC_mirror = http://www.bioconductor.org >>> Change using chooseBioCmirror(). >>> >>> >>>> biocLite("ecoli2.db") >>>> >>>> >>> Using R version 2.12.0, biocinstall version 2.7.4. >>> Installing Bioconductor version 2.7 packages: >>> [1] "ecoli2.db" >>> Please wait... >>> >>> Message d'avis : >>> In getDependencies(pkgs, dependencies, available, lib) : >>> package ?ecoli2.db? is not available >>> >>> Could you please tell me if I am doing something wrong of if this come >>> from a Bioconductor problem that you can fix? >>> >>> Thanks for your precious help, >>> >>> Cl?mentine >>> >>> >>> >>> >>> On Fri, 15 Oct 2010 09:09:40 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> >>> wrote: >>> >>> >>>> Hi Cl?mentine, >>>> >>>> That is probably because I have dropped it into the devel branch. I >>>> will become the release branch next week. I think that most people >>>> > are > >>>> like you and will only care about the K12 strain. But I have to post >>>> > a > >>>> disclaimer (and one is planned for when the package loads), simply >>>> because the probes on this platform were planned for detecting 4 >>>> strains, and we only have annotation for the popular one here. >>>> >>>> >>>> Marc >>>> >>>> >>>> >>>> On 10/15/2010 02:10 AM, Cl?mentine Dressaire wrote: >>>> >>>> >>>>> Dear Marc, >>>>> >>>>> Since I work with the MG1655 (K12) strain it should be enough for me >>>>> > to > >>>>> have only annotations for this one. >>>>> Nevertheless I cannot find the ecoli2 chip package you added neither >>>>> > in > >>>>> Bioconductor website nor using AnnotationDbi package in R. Does it >>>>> > mean > >>>>> that it has not been released yeat or that I have to use the >>>>> ecoliK12.db0? >>>>> Unlesss I am not looking in the right place? >>>>> >>>>> Thanks for your help, be sure it is usefull! >>>>> >>>>> Cl?mentine >>>>> >>>>> >>>>> On Thu, 14 Oct 2010 13:50:43 -0700, Marc Carlson <mcarlson at="" fhcrc.org=""> >>>>> wrote: >>>>> >>>>> >>>>> >>>>>> Hi Cl?mentine, >>>>>> >>>>>> There is both an org package for E coli and also a .db0 package. >>>>>> > The > >>>>>> existence of the .db0 package means that you can use the vignette >>>>>> >>>>>> >>> titled >>> >>> >>>>>> "SQLForge: An easy way to create a new annotation package with a >>>>>> standard database schema." in the AnnotationDbi package to generate >>>>>> > a > >>>>>> chip package for E coli. You can find it here: >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>> > http://www.bioconductor.org/help/bioc- views/devel/bioc/html/AnnotationDbi.html > >>> >>> >>>>> >>>>> >>>>> >>>>>> But since this is an affymetrix package, I just went ahead and added >>>>>> >>>>>> >>> an >>> >>> >>>>>> ecoli2 chip package to the repository for you. >>>>>> >>>>>> Be forewarned though, that while this platform has probes to measure >>>>>> > 4 > >>>>>> different strains of E coli, I can only used the annotations for the >>>>>> popular K12 strain to make this package. If you want to get >>>>>> >>>>>> >>> additional >>> >>> >>>>>> annotations for the other strains, you might be able to get one more >>>>>> >>>>>> >>> in >>> >>> >>>>>> a separate package (if one of the strains is the Sakai strain), but >>>>>> after that things become much more difficult to support... Be sure >>>>>> > to > >>>>>> let us know whether or not this meets your needs. The annotations >>>>>> > are > >>>>>> always a work in progress and we always benefit from feedback to >>>>>> indicate what people are using, and what things might be missing. >>>>>> >>>>>> >>>>>> Marc >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> On 10/14/2010 02:43 AM, Cl?mentine Dressaire wrote: >>>>>> >>>>>> >>>>>> >>>>>>> Dear BioC members, >>>>>>> >>>>>>> >>>>>>> >>>>>>> I was looking for a ecoli2.db annotation file but could not find it >>>>>>> >>>>>>> >>> in >>> >>> >>>>>>> Bioconductor (or elsewhere). From previous posts I saw that some >>>>>>> >>>>>>> >>> people >>> >>> >>>>>>> have already asked for this and were considering creating one. Can >>>>>>> >>>>>>> >>>>>>> >>>>> anyone >>>>> >>>>> >>>>> >>>>>>> tell me if such a work is in process or still a project? If not I >>>>>>> >>>>>>> >>> will >>> >>> >>>>>>> try >>>>>>> >>>>>>> to create my own. Is SQLForge package the most appropriated for >>>>>>> > this > >>>>>>> purpose taking into account that I only have Affymetrix annotation >>>>>>> >>>>>>> >>>>>>> >>>>> file? >>>>> >>>>> >>>>> >>>>>>> With adavanced thanks for your help, >>>>>>> >>>>>>> >>>>>>> >>>>>>> Cl?mentine. >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> _______________________________________________ >>>>>> 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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