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an error in AnnotationForge

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wang peter ★ 2.0k

@wang-peter-4647

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source("http://bioconductor.org/biocLite.R"); biocLite("human.db0"); biocLite("AnnotationDbi"); biocLite("AnnotationForge"); library(human.db0); library(AnnotationDbi); library(AnnotationForge); > available.chipdbschemas(); > dir.create("primeview"); > populateDB("HUMANCHIP_DB",affy=F,prefix="primeview",fileName="primevie wHumanGeneExprs.txt",metaDataSrc=c("DBSCHEMA"="HUMANCHIP_DB","ORGANISM "="Homo sapiens","SPECIES"="Human","MANUFACTURER"="Affymetrix","CHIPNAME"="Pri meView Human Gene Expression Array","MANUFACTURERURL"="http://www.affymetrix.com "),baseMapType="eg",outputDir="primeview"); > seed<-new("AnnDbPkgSeed",Package = "primeview.db",Version="1.0.0",PkgTemplate="HUMANCHIP.DB",AnnObjPrefix ="primeview"); > makeAnnDbPkg(seed,file.path("primeview","primeview.sqlite"),dest_dir=" primeview"); Error in match(x, table, nomatch = 0L) : object 'doc_template_names' not found > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] AnnotationForge_1.2.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.3 DBI_0.2-5 human.db0_2.9.0 [6] AnnotationDbi_1.22.1 Biobase_2.20.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] IRanges_1.18.0 stats4_3.0.0 tools_3.0.0 -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute for Plant Research Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839@cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253 [[alternative HTML version deleted]]

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ADD COMMENT • link updated 11.6 years ago by James W. MacDonald 67k • written 11.6 years ago by wang peter ★ 2.0k

score 0 · Answer 1 · 2013-04-22

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 3 days ago

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Hi Peter, On 4/21/2013 10:25 PM, Wang Peter wrote: > source("http://bioconductor.org/biocLite.R"); > biocLite("human.db0"); > biocLite("AnnotationDbi"); > biocLite("AnnotationForge"); > library(human.db0); > library(AnnotationDbi); > library(AnnotationForge); First, this isn't Perl, so adding in extraneous semi-colons isn't necessary. >> available.chipdbschemas(); >> dir.create("primeview"); >> > populateDB("HUMANCHIP_DB",affy=F,prefix="primeview",fileName="primev iewHumanGeneExprs.txt",metaDataSrc=c("DBSCHEMA"="HUMANCHIP_DB","ORGANI SM"="Homo > sapiens","SPECIES"="Human","MANUFACTURER"="Affymetrix","CHIPNAME"="P rimeView > Human Gene Expression Array","MANUFACTURERURL"="http://www.affymetrix.com > "),baseMapType="eg",outputDir="primeview"); You are using arguments for makeDBPackage, but calling populateDB. There is no reason that I can think of that you should be using populateDB directly, unless you just want the sqlite database. I have no idea why you are doing things this way - why not just follow the vignette? In addition, about half of your arguments are all caps, and are quoted. There are no all caps arguments for any of the functions you are trying to use, nor are there any quoted arguments in R. I would recommend just following the vignette. Also, IIRC the primeview chip is just a 3'-biased array, so you can probably also set affy = TRUE and have the parsing of the file done automatically. Best, Jim >> seed<-new("AnnDbPkgSeed",Package = > "primeview.db",Version="1.0.0",PkgTemplate="HUMANCHIP.DB",AnnObjPref ix="primeview"); > makeAnnDbPkg(seed,file.path("primeview","primeview.sqlite"),dest_dir ="primeview"); > Error in match(x, table, nomatch = 0L) : > object 'doc_template_names' not found >> sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods base > > other attached packages: > [1] AnnotationForge_1.2.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.3 DBI_0.2-5 > human.db0_2.9.0 > [6] AnnotationDbi_1.22.1 Biobase_2.20.0 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] IRanges_1.18.0 stats4_3.0.0 tools_3.0.0 > > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099

ADD COMMENT • link 11.6 years ago James W. MacDonald 67k

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Hi Peter, Maybe this will help you? http://www.bioconductor.org/packages/2.12/bioc/vignettes/AnnotationFor ge/inst/doc/SQLForge.pdf Almost all of the packages in Bioconductor have vignettes, which you can find by navigating to them by using the web site here: http://www.bioconductor.org/packages/2.12/BiocViews.html And then clicking on their various landing pages. OR you can navigate to them by using help.start() to display the documentation for packages that you have installed. Marc On 04/22/2013 07:26 AM, James W. MacDonald wrote: > Hi Peter, > > On 4/21/2013 10:25 PM, Wang Peter wrote: >> source("http://bioconductor.org/biocLite.R"); >> biocLite("human.db0"); >> biocLite("AnnotationDbi"); >> biocLite("AnnotationForge"); >> library(human.db0); >> library(AnnotationDbi); >> library(AnnotationForge); > > First, this isn't Perl, so adding in extraneous semi-colons isn't > necessary. > >>> available.chipdbschemas(); >>> dir.create("primeview"); >>> >> populateDB("HUMANCHIP_DB",affy=F,prefix="primeview",fileName="prime viewHumanGeneExprs.txt",metaDataSrc=c("DBSCHEMA"="HUMANCHIP_DB","ORGAN ISM"="Homo >> >> sapiens","SPECIES"="Human","MANUFACTURER"="Affymetrix","CHIPNAME"=" PrimeView >> >> Human Gene Expression >> Array","MANUFACTURERURL"="http://www.affymetrix.com >> "),baseMapType="eg",outputDir="primeview"); > > You are using arguments for makeDBPackage, but calling populateDB. > There is no reason that I can think of that you should be using > populateDB directly, unless you just want the sqlite database. I have > no idea why you are doing things this way - why not just follow the > vignette? > > In addition, about half of your arguments are all caps, and are > quoted. There are no all caps arguments for any of the functions you > are trying to use, nor are there any quoted arguments in R. > > I would recommend just following the vignette. Also, IIRC the > primeview chip is just a 3'-biased array, so you can probably also set > affy = TRUE and have the parsing of the file done automatically. > > Best, > > Jim > > > >>> seed<-new("AnnDbPkgSeed",Package = >> "primeview.db",Version="1.0.0",PkgTemplate="HUMANCHIP.DB",AnnObjPre fix="primeview"); >> >> makeAnnDbPkg(seed,file.path("primeview","primeview.sqlite"),dest_di r="primeview"); >> >> Error in match(x, table, nomatch = 0L) : >> object 'doc_template_names' not found >>> sessionInfo() >> R version 3.0.0 (2013-04-03) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] AnnotationForge_1.2.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.3 DBI_0.2-5 >> human.db0_2.9.0 >> [6] AnnotationDbi_1.22.1 Biobase_2.20.0 BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] IRanges_1.18.0 stats4_3.0.0 tools_3.0.0 >> >> >

ADD REPLY • link 11.6 years ago Marc Carlson ★ 7.2k

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thank u very much shan On Mon, Apr 22, 2013 at 12:57 PM, Marc Carlson <mcarlson@fhcrc.org> wrote: > Hi Peter, > > Maybe this will help you? > > http://www.bioconductor.org/**packages/2.12/bioc/vignettes/** > AnnotationForge/inst/doc/**SQLForge.pdf<http: www.bioconductor.org="" packages="" 2.12="" bioc="" vignettes="" annotationforge="" inst="" doc="" sqlforge.pdf=""> > > Almost all of the packages in Bioconductor have vignettes, which you can > find by navigating to them by using the web site here: > > http://www.bioconductor.org/**packages/2.12/BiocViews.html<http: ww="" w.bioconductor.org="" packages="" 2.12="" biocviews.html=""> > > And then clicking on their various landing pages. > > > OR you can navigate to them by using help.start() to display the > documentation for packages that you have installed. > > > Marc > > > > > On 04/22/2013 07:26 AM, James W. MacDonald wrote: > >> Hi Peter, >> >> On 4/21/2013 10:25 PM, Wang Peter wrote: >> >>> source("http://bioconductor.**org/biocLite.R<http: bioconductor.o="" rg="" bioclite.r=""> >>> "); >>> biocLite("human.db0"); >>> biocLite("AnnotationDbi"); >>> biocLite("AnnotationForge"); >>> library(human.db0); >>> library(AnnotationDbi); >>> library(AnnotationForge); >>> >> >> First, this isn't Perl, so adding in extraneous semi-colons isn't >> necessary. >> >> available.chipdbschemas(); >>>> dir.create("primeview"); >>>> >>>> populateDB("HUMANCHIP_DB",**affy=F,prefix="primeview",**fileName="** >>> primeviewHumanGeneExprs.txt",**metaDataSrc=c("DBSCHEMA"="**HUMANCH IP_DB","ORGANISM"="Homo >>> >>> sapiens","SPECIES"="Human","**MANUFACTURER"="Affymetrix","**CHIPNA ME"="PrimeView >>> >>> Human Gene Expression Array","MANUFACTURERURL"="http** >>> ://www.affymetrix.com <http: www.affymetrix.com=""> >>> "),baseMapType="eg",outputDir=**"primeview"); >>> >> >> You are using arguments for makeDBPackage, but calling populateDB. There >> is no reason that I can think of that you should be using populateDB >> directly, unless you just want the sqlite database. I have no idea why you >> are doing things this way - why not just follow the vignette? >> >> In addition, about half of your arguments are all caps, and are quoted. >> There are no all caps arguments for any of the functions you are trying to >> use, nor are there any quoted arguments in R. >> >> I would recommend just following the vignette. Also, IIRC the primeview >> chip is just a 3'-biased array, so you can probably also set affy = TRUE >> and have the parsing of the file done automatically. >> >> Best, >> >> Jim >> >> >> >> seed<-new("AnnDbPkgSeed",**Package = >>>> >>> "primeview.db",Version="1.0.0"**,PkgTemplate="HUMANCHIP.DB",**AnnO bjPrefix="primeview"); >>> >>> makeAnnDbPkg(seed,file.path("**primeview","primeview.sqlite")**,de st_dir="primeview"); >>> >>> Error in match(x, table, nomatch = 0L) : >>> object 'doc_template_names' not found >>> >>>> sessionInfo() >>>> >>> R version 3.0.0 (2013-04-03) >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.**UTF-8/C/en_US.UTF-8/en_US.UTF-**8 >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] AnnotationForge_1.2.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.3 DBI_0.2-5 >>> human.db0_2.9.0 >>> [6] AnnotationDbi_1.22.1 Biobase_2.20.0 BiocGenerics_0.6.0 >>> >>> loaded via a namespace (and not attached): >>> [1] IRanges_1.18.0 stats4_3.0.0 tools_3.0.0 >>> >>> >>> >> > ______________________________**_________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.et="" hz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane.** > science.biology.informatics.**conductor<http: news.gmane.org="" gmane.="" science.biology.informatics.conductor=""> > -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute for Plant Research Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839@cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253 [[alternative HTML version deleted]]

ADD REPLY • link 11.6 years ago wang peter ★ 2.0k