Hello group, Has anyone tried to use the updated brainarray files? I have searched the mail lists and this is the most recent thread regarding them, and I found no mention of changes in usage anywhere. I updated to v14.1.0 for hgu133a2hsrefseq and it loads properly: > library(hgu133a2hsrefseq.db) Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation("pkgname")'. Loading required package: org.Hs.eg.db Loading required package: DBI As it states in the instrurctions (and as it has worked before updating), I enter the command data at cdfName = 'hgu133a2hsrefseqREFSEQ' But I get an error when attempting to do rma: > data.rma=rma(data) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain hgu133a2hsrefseqREFSEQ Library - package hgu133a2hsrefseqrefseqcdf not installed Bioconductor - hgu133a2hsrefseqrefseqcdf not available This code has worked flawlessly before so I am not sure what is going on as it appears to have installed and loaded properly!! Thanks in advance for any help! Here is my session info: > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-pc-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] simpleaffy_2.28.0 gcrma_2.24.1 genefilter_1.34.0 [4] affy_1.30.0 hgu133a2hsrefseq.db_14.1.0 org.Hs.eg.db_2.5.0 [7] RSQLite_0.9-4 DBI_0.2-5 AnnotationDbi_1.14.1 [10] Biobase_2.12.1 loaded via a namespace (and not attached): [1] affyio_1.20.0 annotate_1.30.0 Biostrings_2.20.0 IRanges_1.10.0 [5] preprocessCore_1.14.0 splines_2.13.0 survival_2.36-9 tools_2.13.0 [9] xtable_1.5-6 thanks, Mikki On Thu, Apr 21, 2011 at 2:59 PM, Marc Carlson <mcarlson at="" fhcrc.org=""> wrote: > Hi Diego, > > Your requests must have been persuasive since the maintainers at MBNI have > just updated all of their packages again. ?And so there is now a version of > these packages available for Bioconductor 2.8 (R 2.13). > > biocLite() has been updated accordingly and so now you should be able to get > these packages in the very latest release of Bioconductor. > > > ?Marc > > > On 04/20/2011 08:54 PM, Diego Diez wrote: >> >> Hi Marc >> >> Of course, I understand (and support) the idea behind biocLite() and >> that for the bioconductor installation to properly work it is needed >> to ensure appropriate version of the packages to be installed. The >> problem here is that the custom cdf packages are not - to the best of >> my understanding- official bioconductor packages, but the repository >> is provided in biocReposList() as a convenience. Therefore the lack of >> support for custom cdf packages in this bioconductor version was not >> mentioned in the release announcement. It may have been worth >> mentioning since this may have a big impact on users. >> >> Obviously, removing the repository while not suitable packages exists >> makes all the sense. However, biocReposList() also provides a >> repository for cran, and any package present in cran will be installed >> by biocLite() whether it is compatible with the bioconductor version >> or not. Even there is a recent thread in the list about an old (non >> compatible) version of the graph package present in cran being >> installed because the official one was missing in the repositories. >> Unfortunately I cannot think on a way to overcome this limitation. >> That being said I myself never had a problem using biocLite() on a >> number of year of use. >> >> Two additional comments: >> >> - The help page for biocReposList() might be a bit old since it lists >> two repositories not presently found: >> ----------- >> oh : URL for Bioc Omegahat package repository. ?This repository >> ? ? ? ? ? contains the versions of Omegahat packages that were tested >> ? ? ? ? ? with the current Bioc release. >> >> li : URL for Bioc Lindsey package repository. >> ------------ >> >> whereas the repository "extra" is missing. >> >> - The cran repository is forced to be "http://cran.fhcrc.org". >> Wouldn't be better to try to get the default CRAN repository selected >> by the user in case that option is set? >> >> >> Anyway, to finish this lengthy email just let you know that I >> contacted the custom cdf people and they are working on providing >> packages for bioconductor 2.8 soon! >> >> Diego >> >> >> On Thu, Apr 21, 2011 at 1:55 AM, Marc Carlson<mcarlson at="" fhcrc.org=""> ?wrote: >>> >>> Hi Diego, >>> >>> You can always throw caution to the wind and just forcibly install any >>> tarball (if downloaded manually). ?Although that would be taking matters >>> into your own hands, and you would obviously have to live with any of the >>> consequences that might result. >>> >>> But you should *not* normally be able to get these package using >>> biocLite() >>> if there is not an appropriate version available. ?This is because >>> correct >>> version matching is part of what people depend on when using biocLite(). >>> ?And in this case the problem is indeed because of the issue that you >>> mentioned. ?The .db packages would have been built using sources >>> appropriate >>> for the Bioc 2.7 and so if you installed them with Bioc 2.8, the GO and >>> KEGG >>> terms etc. would be out of sync with the rest of the build. >>> >>> It is also true that the cdf and probe packages might be ok for some >>> things >>> in Bioc 2.8. ?But without the corresponding .db package you will not >>> really >>> be able to really use them fully. ?And if you did use them and then tried >>> to >>> use those remapped probe and cdf packages with the wrong (default) .db >>> style >>> packages the result could be quite chaotic. ?So I can't really recommend >>> that either unless you have some very specialized usage in mind. >>> >>> >>> ?Marc >>> >>> >>> >>> >>> On 04/19/2011 07:29 PM, Diego Diez wrote: >>>> >>>> Hi Marc >>>> >>>> On Wed, Apr 20, 2011 at 1:10 AM, Marc Carlson<mcarlson at="" fhcrc.org=""> >>>> ?wrote: >>>>> >>>>> Hi Diego, >>>>> >>>>> The brainarray CDFs are only missing from the 2.8 build of Bioconductor >>>>> because there is not yet a brainarray build that matches that. ?There >>>>> is >>>>> a >>>>> recent brainarray build that matches Bioconductor 2.7 though, so we >>>>> have >>>>> of >>>>> course provided access to that for the older 2.7 branch. >>>> >>>> Do you mean that the recent brainarray build was not generated using >>>> the latest versions of the framework in Bioconductor 2.8 (like GO.db, >>>> KEGG.db, etc.)? Because other than that I can install those packages >>>> without problem in R2.13/Bioc2.8. I imagine this may create some >>>> problems with unmatched entries... >>>> >>>>> If you are interested in access to a set of brainarray packages that >>>>> match >>>>> Bioconductor 2.8, then I would recommend that you contact them and let >>>>> them >>>>> know how much you appreciate their hard work. ? ;) >>>> >>>> I will, since I really appreciate their hard work! >>>> >>>>> We will of course make such packages available as soon as it is >>>>> possible >>>>> to >>>>> do so. >>>> >>>> Thank you for the clarification. >>>> >>>> Diego >>>> >>>>> ?Marc >>>>> >>>>> >>>>> On 04/18/2011 11:20 PM, Diego Diez wrote: >>>>>> >>>>>> Hi all, >>>>>> >>>>>> I noticed that the mirror for the custom CDFs available at the >>>>>> BrainArray Microarray laboratory is missing in BioC 2.8, and wonder >>>>>> whether this is intentional and permanent. >>>>>> >>>>>> Thank you, >>>>>> >>>>>> -- >>>>>> Diego Diez, PhD >>>>>> Bioinformatics center, >>>>>> Institute for Chemical Research, >>>>>> Kyoto University. >>>>>> Gokasho, Uji, Kyoto 611-0011 JAPAN >>>>>> diez at kuicr.kyoto-u.ac.jp >>>>>> >>>>>> >>>>>>> library(Biobase) >>>>>> >>>>>> Welcome to Bioconductor >>>>>> >>>>>> ?Vignettes contain introductory material. To view, type >>>>>> ?'browseVignettes()'. To cite Bioconductor, see >>>>>> ?'citation("Biobase")' and for packages 'citation("pkgname")'. >>>>>> >>>>>>> biocReposList() >>>>>> >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?bioc >>>>>> ? ? ? ? ? "http://bioconductor.org/packages/2.8/bioc" >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? aData >>>>>> "http://bioconductor.org/packages/2.8/data/annotation" >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? eData >>>>>> "http://bioconductor.org/packages/2.8/data/experiment" >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? extra >>>>>> ? ? ? ? ?"http://bioconductor.org/packages/2.8/extra" >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ?cran >>>>>> ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? "http://cran.fhcrc.org" >>>>>>> >>>>>>> sessionInfo() >>>>>> >>>>>> R version 2.13.0 Patched (2011-04-13 r55441) >>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>>>> >>>>>> locale: >>>>>> [1] C/UTF-8/C/C/C/C >>>>>> >>>>>> attached base packages: >>>>>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>>>>> >>>>>> other attached packages: >>>>>> [1] Biobase_2.12.1 >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>> > > _______________________________________________ > 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 >

Hi Mikki, First off, please don't hijack other threads. This doesn't have anything to do with the CDF repository for the MBNI cdfs. When you have a new question, send a new email to the list. On 5/5/2011 1:57 PM, M Behnke wrote: > Hello group, > > Has anyone tried to use the updated brainarray files? I have searched > the mail lists and this is the most recent thread regarding them, and > I found no mention of changes in usage anywhere. > > I updated to v14.1.0 for hgu133a2hsrefseq and it loads properly: > >> library(hgu133a2hsrefseq.db) > Loading required package: AnnotationDbi > Loading required package: Biobase > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'browseVignettes()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation("pkgname")'. > > Loading required package: org.Hs.eg.db > Loading required package: DBI > > As it states in the instrurctions (and as it has worked before > updating), I enter the command > data at cdfName = 'hgu133a2hsrefseqREFSEQ' I would be interested to know what instructions advise you to do this. In addition, I would be shocked if this ever actually worked for you (because it really never should have). What you want to be doing is abatch <- ReadAffy(cdfname = "hgu133a2hsrefseq") data.rma <- rma(abatch) and proceeding from there. You might also reconsider using 'data' as a variable name, as data() is a function from base R, so you are relying on R to divine what you mean when you type data at an R prompt. It's usually pretty good, but why take chances? Best, Jim > > But I get an error when attempting to do rma: >> data.rma=rma(data) > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain hgu133a2hsrefseqREFSEQ > Library - package hgu133a2hsrefseqrefseqcdf not installed > Bioconductor - hgu133a2hsrefseqrefseqcdf not available > > This code has worked flawlessly before so I am not sure what is going > on as it appears to have installed and loaded properly!! > > Thanks in advance for any help! > > Here is my session info: >> sessionInfo() > R version 2.13.0 (2011-04-13) > Platform: x86_64-pc-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] simpleaffy_2.28.0 gcrma_2.24.1 > genefilter_1.34.0 > [4] affy_1.30.0 hgu133a2hsrefseq.db_14.1.0 > org.Hs.eg.db_2.5.0 > [7] RSQLite_0.9-4 DBI_0.2-5 > AnnotationDbi_1.14.1 > [10] Biobase_2.12.1 > > loaded via a namespace (and not attached): > [1] affyio_1.20.0 annotate_1.30.0 Biostrings_2.20.0 > IRanges_1.10.0 > [5] preprocessCore_1.14.0 splines_2.13.0 survival_2.36-9 > tools_2.13.0 > [9] xtable_1.5-6 > > > > > thanks, > Mikki > > On Thu, Apr 21, 2011 at 2:59 PM, Marc Carlson<mcarlson at="" fhcrc.org=""> wrote: >> Hi Diego, >> >> Your requests must have been persuasive since the maintainers at MBNI have >> just updated all of their packages again. And so there is now a version of >> these packages available for Bioconductor 2.8 (R 2.13). >> >> biocLite() has been updated accordingly and so now you should be able to get >> these packages in the very latest release of Bioconductor. >> >> >> Marc >> >> >> On 04/20/2011 08:54 PM, Diego Diez wrote: >>> >>> Hi Marc >>> >>> Of course, I understand (and support) the idea behind biocLite() and >>> that for the bioconductor installation to properly work it is needed >>> to ensure appropriate version of the packages to be installed. The >>> problem here is that the custom cdf packages are not - to the best of >>> my understanding- official bioconductor packages, but the repository >>> is provided in biocReposList() as a convenience. Therefore the lack of >>> support for custom cdf packages in this bioconductor version was not >>> mentioned in the release announcement. It may have been worth >>> mentioning since this may have a big impact on users. >>> >>> Obviously, removing the repository while not suitable packages exists >>> makes all the sense. However, biocReposList() also provides a >>> repository for cran, and any package present in cran will be installed >>> by biocLite() whether it is compatible with the bioconductor version >>> or not. Even there is a recent thread in the list about an old (non >>> compatible) version of the graph package present in cran being >>> installed because the official one was missing in the repositories. >>> Unfortunately I cannot think on a way to overcome this limitation. >>> That being said I myself never had a problem using biocLite() on a >>> number of year of use. >>> >>> Two additional comments: >>> >>> - The help page for biocReposList() might be a bit old since it lists >>> two repositories not presently found: >>> ----------- >>> oh : URL for Bioc Omegahat package repository. This repository >>> contains the versions of Omegahat packages that were tested >>> with the current Bioc release. >>> >>> li : URL for Bioc Lindsey package repository. >>> ------------ >>> >>> whereas the repository "extra" is missing. >>> >>> - The cran repository is forced to be "http://cran.fhcrc.org". >>> Wouldn't be better to try to get the default CRAN repository selected >>> by the user in case that option is set? >>> >>> >>> Anyway, to finish this lengthy email just let you know that I >>> contacted the custom cdf people and they are working on providing >>> packages for bioconductor 2.8 soon! >>> >>> Diego >>> >>> >>> On Thu, Apr 21, 2011 at 1:55 AM, Marc Carlson<mcarlson at="" fhcrc.org=""> wrote: >>>> >>>> Hi Diego, >>>> >>>> You can always throw caution to the wind and just forcibly install any >>>> tarball (if downloaded manually). Although that would be taking matters >>>> into your own hands, and you would obviously have to live with any of the >>>> consequences that might result. >>>> >>>> But you should *not* normally be able to get these package using >>>> biocLite() >>>> if there is not an appropriate version available. This is because >>>> correct >>>> version matching is part of what people depend on when using biocLite(). >>>> And in this case the problem is indeed because of the issue that you >>>> mentioned. The .db packages would have been built using sources >>>> appropriate >>>> for the Bioc 2.7 and so if you installed them with Bioc 2.8, the GO and >>>> KEGG >>>> terms etc. would be out of sync with the rest of the build. >>>> >>>> It is also true that the cdf and probe packages might be ok for some >>>> things >>>> in Bioc 2.8. But without the corresponding .db package you will not >>>> really >>>> be able to really use them fully. And if you did use them and then tried >>>> to >>>> use those remapped probe and cdf packages with the wrong (default) .db >>>> style >>>> packages the result could be quite chaotic. So I can't really recommend >>>> that either unless you have some very specialized usage in mind. >>>> >>>> >>>> Marc >>>> >>>> >>>> >>>> >>>> On 04/19/2011 07:29 PM, Diego Diez wrote: >>>>> >>>>> Hi Marc >>>>> >>>>> On Wed, Apr 20, 2011 at 1:10 AM, Marc Carlson<mcarlson at="" fhcrc.org=""> >>>>> wrote: >>>>>> >>>>>> Hi Diego, >>>>>> >>>>>> The brainarray CDFs are only missing from the 2.8 build of Bioconductor >>>>>> because there is not yet a brainarray build that matches that. There >>>>>> is >>>>>> a >>>>>> recent brainarray build that matches Bioconductor 2.7 though, so we >>>>>> have >>>>>> of >>>>>> course provided access to that for the older 2.7 branch. >>>>> >>>>> Do you mean that the recent brainarray build was not generated using >>>>> the latest versions of the framework in Bioconductor 2.8 (like GO.db, >>>>> KEGG.db, etc.)? Because other than that I can install those packages >>>>> without problem in R2.13/Bioc2.8. I imagine this may create some >>>>> problems with unmatched entries... >>>>> >>>>>> If you are interested in access to a set of brainarray packages that >>>>>> match >>>>>> Bioconductor 2.8, then I would recommend that you contact them and let >>>>>> them >>>>>> know how much you appreciate their hard work. ;) >>>>> >>>>> I will, since I really appreciate their hard work! >>>>> >>>>>> We will of course make such packages available as soon as it is >>>>>> possible >>>>>> to >>>>>> do so. >>>>> >>>>> Thank you for the clarification. >>>>> >>>>> Diego >>>>> >>>>>> Marc >>>>>> >>>>>> >>>>>> On 04/18/2011 11:20 PM, Diego Diez wrote: >>>>>>> >>>>>>> Hi all, >>>>>>> >>>>>>> I noticed that the mirror for the custom CDFs available at the >>>>>>> BrainArray Microarray laboratory is missing in BioC 2.8, and wonder >>>>>>> whether this is intentional and permanent. >>>>>>> >>>>>>> Thank you, >>>>>>> >>>>>>> -- >>>>>>> Diego Diez, PhD >>>>>>> Bioinformatics center, >>>>>>> Institute for Chemical Research, >>>>>>> Kyoto University. >>>>>>> Gokasho, Uji, Kyoto 611-0011 JAPAN >>>>>>> diez at kuicr.kyoto-u.ac.jp >>>>>>> >>>>>>> >>>>>>>> library(Biobase) >>>>>>> >>>>>>> Welcome to Bioconductor >>>>>>> >>>>>>> Vignettes contain introductory material. To view, type >>>>>>> 'browseVignettes()'. To cite Bioconductor, see >>>>>>> 'citation("Biobase")' and for packages 'citation("pkgname")'. >>>>>>> >>>>>>>> biocReposList() >>>>>>> >>>>>>> bioc >>>>>>> "http://bioconductor.org/packages/2.8/bioc" >>>>>>> aData >>>>>>> "http://bioconductor.org/packages/2.8/data/annotation" >>>>>>> eData >>>>>>> "http://bioconductor.org/packages/2.8/data/experiment" >>>>>>> extra >>>>>>> "http://bioconductor.org/packages/2.8/extra" >>>>>>> cran >>>>>>> "http://cran.fhcrc.org" >>>>>>>> >>>>>>>> sessionInfo() >>>>>>> >>>>>>> R version 2.13.0 Patched (2011-04-13 r55441) >>>>>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>>>>> >>>>>>> locale: >>>>>>> [1] C/UTF-8/C/C/C/C >>>>>>> >>>>>>> attached base packages: >>>>>>> [1] stats graphics grDevices utils datasets methods base >>>>>>> >>>>>>> other attached packages: >>>>>>> [1] Biobase_2.12.1 >>>>>>> >>>>>>> _______________________________________________ >>>>>>> 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 >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>>> >>>> >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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. 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