It looks like affylmGUI (maintainer CC'd) still has a lot of calls to Biobase:::biocReposList() which is indeed a defunct function. It should use BiocInstaller biocinstallRepos() instead. Dan On Thu, Jul 5, 2012 at 2:47 PM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > Hi Burkhard, > > Well, that all looks OK. So the next likely culprit is affylmGUI itself. > Since you are not getting the gene symbols, it would be reasonable to assume > that affylmGUI is trying to download and install the correct annotation > package. > > You don't say what chip data you are analyzing, so I can't give much more > than a generalized pointer. If it is an old-school 3'-biased chip (like the > HG-U133 plus 2 chip), then you can usually get really close to the right > name by just reducing to lower case and removing all punctuation, then > adding a .db, so e.g, hgu133plus2.db is the annotation package. If you are > using a Gene ST package, then you want to do the same, but add > transcriptcluster.db. So e.g., the HuGene 1.0 ST chip annotation package is > the hugene10sttranscriptcluster.db. > > So try installing the correct annotation package first, then do your > analysis. See if that helps. > > Best, > > Jim > > > > On 7/5/2012 4:54 PM, Burkhard Heil wrote: >> >> Hi Jim, >> >> Thanks for your quick reply. Here is the Output of sessionInfo: >> >> >> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] tcltk stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] affylmGUI_1.30.0 affyio_1.24.0 affy_1.34.0 >> Biobase_2.16.0 >> [5] BiocGenerics_0.2.0 limma_3.12.1 stringr_0.6 >> >> loaded via a namespace (and not attached): >> [1] BiocInstaller_1.4.7 plyr_1.7.1 preprocessCore_1.18.0 >> [4] zlibbioc_1.2.0 >> Cheers >> Burkhard >> >> >> On 05.07.2012, at 21:05, "James W. MacDonald"<jmacdon at="" uw.edu=""> wrote: >> >> >>> HI Burkhard, >>> >>> On 7/5/2012 9:24 AM, Burkhard Heil wrote: >>>> >>>> Hi everybody, >>>> >>>> when trying to calculate the Toptable in affylmGUI there pops the >>>> following error message up: >>>> >>>> Error: The biocReposList() function is defunct. Please use biocLite() to >>>> install packages source("http://bioconductor.org/biocLite.R") >>>> biocLite("<pkgname>") if you really need to get the list of Bioconductor >>>> package repositories (like biocReposList() does), then do: >>>> source("http://bioconductor.org/biocLite.R") biocinstallRepos() >>>> >>>> The Toptable ist still calculated but without the Gene Symbols. When I >>>> call biocLite() from R, it tries to install the packages 'Biobase' 'IRanges' >>>> and 'AnnotationDbi'. Sounds to me that the last one is causing the problem. >>>> Also, biocLite complains that it can't access >>>> "http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/con trib/2.15". >>>> I read the post about that problem and changed the mirror via >>>> chooseBioCmirror(). biocLite still looks for the brainarray adress but then >>>> install from another mirror. But everytime I call biocLite it installs those >>>> 3 packges. >>>> >>>> I'm running R 2.15.1 on OS X Lion. AffylmGUI and all the relevant >>>> packages should have the most recent version. >>> >>> Should have? That's not very reassuring. Why don't you load affylmGUI, >>> run sessionInfo() and then post the output. >>> >>> Best, >>> >>> Jim >>> >>> >>>> Any help would be greatly appreciated! Thanks >>>> >>>> Burkhard >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> University of Washington >>> Environmental and Occupational Health Sciences >>> 4225 Roosevelt Way NE, # 100 >>> Seattle WA 98105-6099 >>> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > _______________________________________________ > 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 Jin, thanks for your help! It's an HuGene 1.0 ST chip and I downloaded the annotation (to be sure every hugene* annotation package) but I still got the same problem. Just to be sure, by "reducing to lower case and removing...." you don't mean to change anything in the CEL file (or wherever) but just to find the correct annotation package? cheers Burkhard On 05.07.2012, at 23:47, James W. MacDonald wrote: > Hi Burkhard, > > Well, that all looks OK. So the next likely culprit is affylmGUI itself. Since you are not getting the gene symbols, it would be reasonable to assume that affylmGUI is trying to download and install the correct annotation package. > > You don't say what chip data you are analyzing, so I can't give much more than a generalized pointer. If it is an old-school 3'-biased chip (like the HG-U133 plus 2 chip), then you can usually get really close to the right name by just reducing to lower case and removing all punctuation, then adding a .db, so e.g, hgu133plus2.db is the annotation package. If you are using a Gene ST package, then you want to do the same, but add transcriptcluster.db. So e.g., the HuGene 1.0 ST chip annotation package is the hugene10sttranscriptcluster.db. > > So try installing the correct annotation package first, then do your analysis. See if that helps. > > Best, > > Jim > > > > On 7/5/2012 4:54 PM, Burkhard Heil wrote: >> Hi Jim, >> >> Thanks for your quick reply. Here is the Output of sessionInfo: >> >> >> sessionInfo() >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] tcltk stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] affylmGUI_1.30.0 affyio_1.24.0 affy_1.34.0 Biobase_2.16.0 >> [5] BiocGenerics_0.2.0 limma_3.12.1 stringr_0.6 >> >> loaded via a namespace (and not attached): >> [1] BiocInstaller_1.4.7 plyr_1.7.1 preprocessCore_1.18.0 >> [4] zlibbioc_1.2.0 >> Cheers >> Burkhard >> >> >> On 05.07.2012, at 21:05, "James W. MacDonald"<jmacdon at="" uw.edu=""> wrote: >> >>> HI Burkhard, >>> >>> On 7/5/2012 9:24 AM, Burkhard Heil wrote: >>>> Hi everybody, >>>> >>>> when trying to calculate the Toptable in affylmGUI there pops the following error message up: >>>> >>>> Error: The biocReposList() function is defunct. Please use biocLite() to install packages source("http://bioconductor.org/biocLite.R") biocLite("<pkgname>") if you really need to get the list of Bioconductor package repositories (like biocReposList() does), then do: source("http://bioconductor.org/biocLite.R") biocinstallRepos() >>>> >>>> The Toptable ist still calculated but without the Gene Symbols. When I call biocLite() from R, it tries to install the packages 'Biobase' 'IRanges' and 'AnnotationDbi'. Sounds to me that the last one is causing the problem. Also, biocLite complains that it can't access "http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/c ontrib/2.15". I read the post about that problem and changed the mirror via chooseBioCmirror(). biocLite still looks for the brainarray adress but then install from another mirror. But everytime I call biocLite it installs those 3 packges. >>>> >>>> I'm running R 2.15.1 on OS X Lion. AffylmGUI and all the relevant packages should have the most recent version. >>> Should have? That's not very reassuring. Why don't you load affylmGUI, run sessionInfo() and then post the output. >>> >>> Best, >>> >>> Jim >>> >>> >>>> Any help would be greatly appreciated! Thanks >>>> >>>> Burkhard >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> University of Washington >>> Environmental and Occupational Health Sciences >>> 4225 Roosevelt Way NE, # 100 >>> Seattle WA 98105-6099 >>> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 >

Hi Jim, thanks again for all your help. I can't see any messages to R from affylmGUI. But I think the problem is, that for some reason affylmGUI can't identify the correct annotation package for the Chip and tries downloading it yousing defunct procedures. So for now I'll ignore the problem and annotate the top table afterwards. Cheers Burkhard On 06.07.2012, at 15:56, James W. MacDonald wrote: > Hi Burkhard, > > > On 7/6/2012 3:19 AM, Burkhard Heil wrote: >> Hi Jin, >> >> thanks for your help! It's an HuGene 1.0 ST chip and I downloaded the annotation (to be sure every hugene* annotation package) but I still got the same problem. Just to be sure, by "reducing to lower case and removing...." you don't mean to change anything in the CEL file (or wherever) but just to find the correct annotation package? > > Yes, the lower case business is just to help you find the right annotation package. Just to check - are you using one of the brainarray cdfs? If so you need to get their annotation package. > > Also, I have never used affylmGUI, so I am not familiar with the intricacies of using the package. When you are using this package, are there any messages or output posted to the R terminal? Like for instance any messages about what is being downloaded (or attempted to be downloaded)? > > Best, > > Jim > > >> >> cheers >> Burkhard >> >> On 05.07.2012, at 23:47, James W. MacDonald wrote: >> >>> Hi Burkhard, >>> >>> Well, that all looks OK. So the next likely culprit is affylmGUI itself. Since you are not getting the gene symbols, it would be reasonable to assume that affylmGUI is trying to download and install the correct annotation package. >>> >>> You don't say what chip data you are analyzing, so I can't give much more than a generalized pointer. If it is an old-school 3'-biased chip (like the HG-U133 plus 2 chip), then you can usually get really close to the right name by just reducing to lower case and removing all punctuation, then adding a .db, so e.g, hgu133plus2.db is the annotation package. If you are using a Gene ST package, then you want to do the same, but add transcriptcluster.db. So e.g., the HuGene 1.0 ST chip annotation package is the hugene10sttranscriptcluster.db. >>> >>> So try installing the correct annotation package first, then do your analysis. See if that helps. >>> >>> Best, >>> >>> Jim >>> >>> >>> >>> On 7/5/2012 4:54 PM, Burkhard Heil wrote: >>>> Hi Jim, >>>> >>>> Thanks for your quick reply. Here is the Output of sessionInfo: >>>> >>>> >>>> sessionInfo() >>>> R version 2.15.1 (2012-06-22) >>>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >>>> >>>> locale: >>>> [1] C >>>> >>>> attached base packages: >>>> [1] tcltk stats graphics grDevices utils datasets methods >>>> [8] base >>>> >>>> other attached packages: >>>> [1] affylmGUI_1.30.0 affyio_1.24.0 affy_1.34.0 Biobase_2.16.0 >>>> [5] BiocGenerics_0.2.0 limma_3.12.1 stringr_0.6 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] BiocInstaller_1.4.7 plyr_1.7.1 preprocessCore_1.18.0 >>>> [4] zlibbioc_1.2.0 >>>> Cheers >>>> Burkhard >>>> >>>> >>>> On 05.07.2012, at 21:05, "James W. MacDonald"<jmacdon at="" uw.edu=""> wrote: >>>> >>>>> HI Burkhard, >>>>> >>>>> On 7/5/2012 9:24 AM, Burkhard Heil wrote: >>>>>> Hi everybody, >>>>>> >>>>>> when trying to calculate the Toptable in affylmGUI there pops the following error message up: >>>>>> >>>>>> Error: The biocReposList() function is defunct. Please use biocLite() to install packages source("http://bioconductor.org/biocLite.R") biocLite("<pkgname>") if you really need to get the list of Bioconductor package repositories (like biocReposList() does), then do: source("http://bioconductor.org/biocLite.R") biocinstallRepos() >>>>>> >>>>>> The Toptable ist still calculated but without the Gene Symbols. When I call biocLite() from R, it tries to install the packages 'Biobase' 'IRanges' and 'AnnotationDbi'. Sounds to me that the last one is causing the problem. Also, biocLite complains that it can't access "http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/c ontrib/2.15". I read the post about that problem and changed the mirror via chooseBioCmirror(). biocLite still looks for the brainarray adress but then install from another mirror. But everytime I call biocLite it installs those 3 packges. >>>>>> >>>>>> I'm running R 2.15.1 on OS X Lion. AffylmGUI and all the relevant packages should have the most recent version. >>>>> Should have? That's not very reassuring. Why don't you load affylmGUI, run sessionInfo() and then post the output. >>>>> >>>>> Best, >>>>> >>>>> Jim >>>>> >>>>> >>>>>> Any help would be greatly appreciated! Thanks >>>>>> >>>>>> Burkhard >>>>>> >>>>>> _______________________________________________ >>>>>> Bioconductor mailing list >>>>>> Bioconductor at r-project.org >>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>> -- >>>>> James W. MacDonald, M.S. >>>>> Biostatistician >>>>> University of Washington >>>>> Environmental and Occupational Health Sciences >>>>> 4225 Roosevelt Way NE, # 100 >>>>> Seattle WA 98105-6099 >>>>> >>> -- >>> James W. MacDonald, M.S. >>> Biostatistician >>> University of Washington >>> Environmental and Occupational Health Sciences >>> 4225 Roosevelt Way NE, # 100 >>> Seattle WA 98105-6099 >>> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 >