annotation information about ecoli2
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Minwook Kim ▴ 10
@minwook-kim-3126
Last seen 8.1 years ago
Hi, I run the aafTableAnn() to get the annotation information of eocli2. But I got the error. I did try to get the ecoli package. but it failed. Anyone help me? > AnnTable2 <- aafTableAnn(AllGenes,chiptype,AnnCols[2]); Loading required package: ecoli2 Error in aaf.handler(chip = chip) : Couldn't load data package ecoli2 In addition: Warning message: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,? : ? there is no package called 'ecoli2' Apparently, the following information are helpful to fix it. > chiptype [1] "ecoli2" ? "AllGenes" variable includes probe ids. I guess "ecoli2" microarry is not supported by annaffy package. or I don"t know how to download the ecoli2 package. Thanks. Minwook >?sessionInfo() R version 2.7.0 (2008-04-22) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] splines?? tools???? stats???? graphics? grDevices utils???? datasets [8] methods?? base???? other attached packages: ?[1] gplots_2.6.0???????? gdata_2.4.2????????? gtools_2.5.0??????? ?[4] simpleaffy_2.16.1??? ecoli2probe_2.2.0??? ecoli2cdf_2.2.0???? ?[7] bioDist_1.12.0?????? genefilter_1.20.1??? survival_2.34-1???? [10] annaffy_1.12.1?????? KEGG.db_2.2.0??????? GO.db_2.2.0???????? [13] AnnotationDbi_1.2.2? RSQLite_0.7-1??????? DBI_0.2-4?????????? [16] gcrma_2.12.1???????? matchprobes_1.12.1?? affy_1.18.2???????? [19] preprocessCore_1.2.1 affyio_1.8.1???????? Biobase_2.0.1?????? loaded via a namespace (and not attached): [1] annotate_1.18.0
Annotation GO probe annaffy Annotation GO probe annaffy • 774 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States
Hi Minwook, Minwook Kim wrote: > Hi, > I run the aafTableAnn() to get the annotation information of eocli2. > But I got the error. I did try to get the ecoli package. but it failed. Anyone help me? >> AnnTable2 <- aafTableAnn(AllGenes,chiptype,AnnCols[2]); > Loading required package: ecoli2 > Error in aaf.handler(chip = chip) : Couldn't load data package ecoli2 > In addition: Warning message: > In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : > there is no package called 'ecoli2' This is true. In addition, there is no ecoli2.db package, nor can I find any Biomart servers that might help. So for the time being, it appears the best bet for annotation is the annotation file from Affymetrix. http://www.affymetrix.com/Auth/analysis/downloads/na26/ivt/E_coli_2.na 26.annot.csv.zip You can make HTML or text tables using this file and the annotate package if that is what you are trying to do - see the 'Get HTML Output' vignette. Best, Jim > > > Apparently, the following information are helpful to fix it. >> chiptype > [1] "ecoli2" > > "AllGenes" variable includes probe ids. > > I guess "ecoli2" microarry is not supported by annaffy package. or I don"t know how to download the ecoli2 package. > > Thanks. > Minwook > > >> sessionInfo() > R version 2.7.0 (2008-04-22) > x86_64-redhat-linux-gnu > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > other attached packages: > [1] gplots_2.6.0 gdata_2.4.2 gtools_2.5.0 > [4] simpleaffy_2.16.1 ecoli2probe_2.2.0 ecoli2cdf_2.2.0 > [7] bioDist_1.12.0 genefilter_1.20.1 survival_2.34-1 > [10] annaffy_1.12.1 KEGG.db_2.2.0 GO.db_2.2.0 > [13] AnnotationDbi_1.2.2 RSQLite_0.7-1 DBI_0.2-4 > [16] gcrma_2.12.1 matchprobes_1.12.1 affy_1.18.2 > [19] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 > loaded via a namespace (and not attached): > [1] annotate_1.18.0 > > > > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
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Hi guys, You could make a package using the SQLForge code in the AnnotationDbi package. Here is where you can find a vignette to explain how to use it: http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.h tml Marc James W. MacDonald wrote: > Hi Minwook, > > Minwook Kim wrote: >> Hi, >> I run the aafTableAnn() to get the annotation information of eocli2. >> But I got the error. I did try to get the ecoli package. but it >> failed. Anyone help me? >>> AnnTable2 <- aafTableAnn(AllGenes,chiptype,AnnCols[2]); >> Loading required package: ecoli2 >> Error in aaf.handler(chip = chip) : Couldn't load data package ecoli2 >> In addition: Warning message: >> In library(package, lib.loc = lib.loc, character.only = TRUE, >> logical.return = TRUE, : >> there is no package called 'ecoli2' > > This is true. In addition, there is no ecoli2.db package, nor can I > find any Biomart servers that might help. So for the time being, it > appears the best bet for annotation is the annotation file from > Affymetrix. > > http://www.affymetrix.com/Auth/analysis/downloads/na26/ivt/E_coli_2. na26.annot.csv.zip > > > You can make HTML or text tables using this file and the annotate > package if that is what you are trying to do - see the 'Get HTML > Output' vignette. > > Best, > > Jim > > >> >> >> Apparently, the following information are helpful to fix it. >>> chiptype >> [1] "ecoli2" >> >> "AllGenes" variable includes probe ids. >> >> I guess "ecoli2" microarry is not supported by annaffy package. or I >> don"t know how to download the ecoli2 package. >> Thanks. >> Minwook >> >> >>> sessionInfo() >> R version 2.7.0 (2008-04-22) x86_64-redhat-linux-gnu locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=C >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils >> datasets [8] methods base other attached packages: >> [1] gplots_2.6.0 gdata_2.4.2 gtools_2.5.0 >> [4] simpleaffy_2.16.1 ecoli2probe_2.2.0 ecoli2cdf_2.2.0 >> [7] bioDist_1.12.0 genefilter_1.20.1 survival_2.34-1 >> [10] annaffy_1.12.1 KEGG.db_2.2.0 GO.db_2.2.0 >> [13] AnnotationDbi_1.2.2 RSQLite_0.7-1 DBI_0.2-4 >> [16] gcrma_2.12.1 matchprobes_1.12.1 affy_1.18.2 >> [19] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 >> loaded via a namespace (and not attached): >> [1] annotate_1.18.0 >> >> >> >> >> _______________________________________________ >> 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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Thanks, Marc. I know you recently posted on the listserv which species have a .db0 file (and for which a annotation package can be built), but is there somewhere that an updated list is posted of the available species? Best, Jim Marc Carlson wrote: > Hi guys, > > You could make a package using the SQLForge code in the AnnotationDbi > package. Here is where you can find a vignette to explain how to use it: > > http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi .html > > Marc > > > James W. MacDonald wrote: >> Hi Minwook, >> >> Minwook Kim wrote: >>> Hi, >>> I run the aafTableAnn() to get the annotation information of eocli2. >>> But I got the error. I did try to get the ecoli package. but it >>> failed. Anyone help me? >>>> AnnTable2 <- aafTableAnn(AllGenes,chiptype,AnnCols[2]); >>> Loading required package: ecoli2 >>> Error in aaf.handler(chip = chip) : Couldn't load data package ecoli2 >>> In addition: Warning message: >>> In library(package, lib.loc = lib.loc, character.only = TRUE, >>> logical.return = TRUE, : >>> there is no package called 'ecoli2' >> This is true. In addition, there is no ecoli2.db package, nor can I >> find any Biomart servers that might help. So for the time being, it >> appears the best bet for annotation is the annotation file from >> Affymetrix. >> >> http://www.affymetrix.com/Auth/analysis/downloads/na26/ivt/E_coli_2 .na26.annot.csv.zip >> >> >> You can make HTML or text tables using this file and the annotate >> package if that is what you are trying to do - see the 'Get HTML >> Output' vignette. >> >> Best, >> >> Jim >> >> >>> >>> Apparently, the following information are helpful to fix it. >>>> chiptype >>> [1] "ecoli2" >>> >>> "AllGenes" variable includes probe ids. >>> >>> I guess "ecoli2" microarry is not supported by annaffy package. or I >>> don"t know how to download the ecoli2 package. >>> Thanks. >>> Minwook >>> >>> >>>> sessionInfo() >>> R version 2.7.0 (2008-04-22) x86_64-redhat-linux-gnu locale: >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8; LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_ID ENTIFICATION=C >>> >>> attached base packages: >>> [1] splines tools stats graphics grDevices utils >>> datasets [8] methods base other attached packages: >>> [1] gplots_2.6.0 gdata_2.4.2 gtools_2.5.0 >>> [4] simpleaffy_2.16.1 ecoli2probe_2.2.0 ecoli2cdf_2.2.0 >>> [7] bioDist_1.12.0 genefilter_1.20.1 survival_2.34-1 >>> [10] annaffy_1.12.1 KEGG.db_2.2.0 GO.db_2.2.0 >>> [13] AnnotationDbi_1.2.2 RSQLite_0.7-1 DBI_0.2-4 >>> [16] gcrma_2.12.1 matchprobes_1.12.1 affy_1.18.2 >>> [19] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 >>> loaded via a namespace (and not attached): >>> [1] annotate_1.18.0 >>> >>> >>> >>> >>> _______________________________________________ >>> 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 > -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. Medical Center Drive Ann Arbor MI 48109-0646 734-936-8662
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Hi Jim, There is an updated list of supported species in inst/NEWS file for the AnnotationDbi package. You can also just look for appropriate ".db0" files on offer at the web site the way that you could search for a platform specific package. Only the intermediate databases end with the ".db0" extension. http://www.bioconductor.org/packages/release/data/annotation/ Marc James W. MacDonald wrote: > Thanks, Marc. I know you recently posted on the listserv which species > have a .db0 file (and for which a annotation package can be built), > but is there somewhere that an updated list is posted of the available > species? > > Best, > > Jim > > > > Marc Carlson wrote: >> Hi guys, >> >> You could make a package using the SQLForge code in the AnnotationDbi >> package. Here is where you can find a vignette to explain how to use >> it: >> >> http://www.bioconductor.org/packages/release/bioc/html/AnnotationDb i.html >> >> >> Marc >> >> >> James W. MacDonald wrote: >>> Hi Minwook, >>> >>> Minwook Kim wrote: >>>> Hi, >>>> I run the aafTableAnn() to get the annotation information of eocli2. >>>> But I got the error. I did try to get the ecoli package. but it >>>> failed. Anyone help me? >>>>> AnnTable2 <- aafTableAnn(AllGenes,chiptype,AnnCols[2]); >>>> Loading required package: ecoli2 >>>> Error in aaf.handler(chip = chip) : Couldn't load data package ecoli2 >>>> In addition: Warning message: >>>> In library(package, lib.loc = lib.loc, character.only = TRUE, >>>> logical.return = TRUE, : >>>> there is no package called 'ecoli2' >>> This is true. In addition, there is no ecoli2.db package, nor can I >>> find any Biomart servers that might help. So for the time being, it >>> appears the best bet for annotation is the annotation file from >>> Affymetrix. >>> >>> http://www.affymetrix.com/Auth/analysis/downloads/na26/ivt/E_coli_ 2.na26.annot.csv.zip >>> >>> >>> >>> You can make HTML or text tables using this file and the annotate >>> package if that is what you are trying to do - see the 'Get HTML >>> Output' vignette. >>> >>> Best, >>> >>> Jim >>> >>> >>>> >>>> Apparently, the following information are helpful to fix it. >>>>> chiptype >>>> [1] "ecoli2" >>>> >>>> "AllGenes" variable includes probe ids. >>>> >>>> I guess "ecoli2" microarry is not supported by annaffy package. or I >>>> don"t know how to download the ecoli2 package. >>>> Thanks. >>>> Minwook >>>> >>>> >>>>> sessionInfo() >>>> R version 2.7.0 (2008-04-22) x86_64-redhat-linux-gnu locale: >>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE= en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8 ;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_I DENTIFICATION=C >>>> >>>> >>>> attached base packages: >>>> [1] splines tools stats graphics grDevices utils >>>> datasets [8] methods base other attached packages: >>>> [1] gplots_2.6.0 gdata_2.4.2 gtools_2.5.0 >>>> [4] simpleaffy_2.16.1 ecoli2probe_2.2.0 ecoli2cdf_2.2.0 >>>> [7] bioDist_1.12.0 genefilter_1.20.1 survival_2.34-1 >>>> [10] annaffy_1.12.1 KEGG.db_2.2.0 GO.db_2.2.0 >>>> [13] AnnotationDbi_1.2.2 RSQLite_0.7-1 DBI_0.2-4 >>>> [16] gcrma_2.12.1 matchprobes_1.12.1 affy_1.18.2 >>>> [19] preprocessCore_1.2.1 affyio_1.8.1 Biobase_2.0.1 >>>> loaded via a namespace (and not attached): >>>> [1] annotate_1.18.0 >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> 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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Hi Jim, James W. MacDonald wrote: > Thanks, Marc. I know you recently posted on the listserv which species > have a .db0 file (and for which a annotation package can be built), but > is there somewhere that an updated list is posted of the available species? Get the real-time availability with: available.db0pkgs <- function() { url <- "http://bioconductor.org/packages/release/data/annotation/src/contrib" pkgs <- available.packages(url)[, "Package"] pkgs <- pkgs[substr(pkgs, nchar(pkgs)-3, nchar(pkgs)) == ".db0"] names(pkgs) <- NULL pkgs } > available.db0pkgs() [1] "arabidopsis.db0" "bovine.db0" "canine.db0" "chicken.db0" [5] "ecoliK12.db0" "ecoliSakai.db0" "fly.db0" "human.db0" [9] "malaria.db0" "mouse.db0" "pig.db0" "rat.db0" [13] "worm.db0" "yeast.db0" "zebrafish.db0" Cheers, H.
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