Having trouble with new brainarray CDF
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Entering edit mode
Martha Behnke ▴ 100
@martha-behnke-3807
Last seen 7.1 years ago
My apologies, the subject line and discussion were about the brainarray CDFs and the fact that they were now updated, and my problem is with the updates so the background seemed appropriate. I've changed the subject line now. Thank you for responding so quickly, however, using the code you suggest gives me the same error: > abatch <- ReadAffy(cdfname = "hgu133a2hsrefseq") > data.rma <- rma(abatch) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain hgu133a2hsrefseq Library - package hgu133a2hsrefseqcdf not installed Bioconductor - hgu133a2hsrefseqcdf not available I got my original code from the paper referenced on the brainarray website http://nar.oxfordjournals.org/content/33/20/e175.full?ijkey=zaJMV7qU1X ANIci&keytype=ref under the section "Use of custom CDF" The previous version (2.12 and appropriate cdf) continues to work with either code. I checked help(package=...) to make sure I wasn't referencing it wong, but I don't see any problems with the names... Information on package 'hgu133a2hsrefseq.db' Description: Package: hgu133a2hsrefseq.db Title: Affymetrix hgu133a2 annotation data (chip hgu133a2hsrefseq) Description: Affymetrix hgu133a2 annotation data (chip hgu133a2hsrefseq) assembled using data from public repositories Version: 14.1.0 Author: Marc Carlson, Seth Falcon, Herve Pages, Nianhua Li Maintainer: Biocore Data Team <biocannotation at="" lists.fhcrc.org=""> Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.14.1), org.Hs.eg.db (>= 2.5.0) Suggests: annotate Imports: methods, AnnotationDbi License: Artistic-2.0 organism: Homo sapiens species: Human manufacturer: Affymetrix chipName: hgu133a2 manufacturerUrl: http://www.affymetrix.com biocViews: AnnotationData, AffymetrixChip, Homo_sapiens, hgu133a2hsrefseq Packaged: 2011-04-21 03:01:18 UTC; daimh Built: R 2.13.0; ; 2011-05-05 17:36:07 UTC; windows Index: hgu133a2hsrefseq.db Bioconductor annotation data package hgu133a2hsrefseqREFSEQ Map between Manufacturer Identifiers and RefSeq Identifiers hgu133a2hsrefseqSYMBOL Map between Manufacturer Identifiers and Gene Symbols Thanks again! Mikki On Thu, May 5, 2011 at 3:06 PM, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > 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. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues >
Microarray Annotation AnnotationData AffymetrixChip hgu133a2 cdf probe graph AnnotationDbi • 1.4k views
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Entering edit mode
Marc Carlson ★ 7.2k
@marc-carlson-2264
Last seen 5.2 years ago
United States
Hi Mikki, Have you tried also updating the matching cdf file (as suggested by the error message: "Library - package hgu133a2hsrefseqcdf not installed")? IOW:||| source("http://bioconductor.org/biocLite.R")| biocLite("hgu133a2hsrefseqcdf") Marc On 05/05/2011 12:33 PM, M Behnke wrote: > My apologies, the subject line and discussion were about the > brainarray CDFs and the fact that they were now updated, and my > problem is with the updates so the background seemed appropriate. > I've changed the subject line now. > > Thank you for responding so quickly, however, using the code you > suggest gives me the same error: > >> abatch<- ReadAffy(cdfname = "hgu133a2hsrefseq") >> data.rma<- rma(abatch) > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain hgu133a2hsrefseq > Library - package hgu133a2hsrefseqcdf not installed > Bioconductor - hgu133a2hsrefseqcdf not available > > I got my original code from the paper referenced on the brainarray website > http://nar.oxfordjournals.org/content/33/20/e175.full?ijkey=zaJMV7qU 1XANIci&keytype=ref > under the section "Use of custom CDF" > > The previous version (2.12 and appropriate cdf) continues to work with > either code. > > I checked help(package=...) to make sure I wasn't referencing it wong, > but I don't see any problems with the names... > > Information on package 'hgu133a2hsrefseq.db' > > Description: > > Package: hgu133a2hsrefseq.db > Title: Affymetrix hgu133a2 annotation data (chip > hgu133a2hsrefseq) > Description: Affymetrix hgu133a2 annotation data (chip > hgu133a2hsrefseq) assembled using data from public > repositories > Version: 14.1.0 > Author: Marc Carlson, Seth Falcon, Herve Pages, Nianhua Li > Maintainer: Biocore Data Team<biocannotation@lists.fhcrc.org> > Depends: R (>= 2.7.0), methods, AnnotationDbi (>= 1.14.1), > org.Hs.eg.db (>= 2.5.0) > Suggests: annotate > Imports: methods, AnnotationDbi > License: Artistic-2.0 > organism: Homo sapiens > species: Human > manufacturer: Affymetrix > chipName: hgu133a2 > manufacturerUrl: http://www.affymetrix.com > biocViews: AnnotationData, AffymetrixChip, Homo_sapiens, > hgu133a2hsrefseq > Packaged: 2011-04-21 03:01:18 UTC; daimh > Built: R 2.13.0; ; 2011-05-05 17:36:07 UTC; windows > > Index: > > hgu133a2hsrefseq.db Bioconductor annotation data package > hgu133a2hsrefseqREFSEQ > Map between Manufacturer Identifiers and RefSeq > Identifiers > hgu133a2hsrefseqSYMBOL > Map between Manufacturer Identifiers and Gene > Symbols > > Thanks again! > Mikki > > On Thu, May 5, 2011 at 3:06 PM, James W. MacDonald > <jmacdon@med.umich.edu> wrote: >> 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@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@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@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@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@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@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@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@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@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 >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> > _______________________________________________ > 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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