how to add a table to AnnotationDbi sqlite database?

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Dana.Stanley@csiro.au ▴ 110

@danastanleycsiroau-3979

Last seen 9.6 years ago

Hi all I am trying to use goProfyles with my custom chicken database GGal.db. The package is looking for the file in my database that does not exist : Error in eval(expr, envir, enclos) : object 'GGal.dbENTREZID' not found I can make a simple table linking my ID and entrez id that the package is looking for, but I could not figure out how to add it to the database... To all of you reading posts and helping others a big THANKS. Dana [[alternative HTML version deleted]]

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ADD COMMENT • link 12.4 years ago Dana.Stanley@csiro.au ▴ 110

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Marc Carlson ★ 7.2k

@marc-carlson-2264

Last seen 7.7 years ago

United States

Hi Dana, I want to help you, but I need to know a lot more information before I can do so. So please excuse me while I ask you a ton of questions: What is your sessionInfo? Do you have a reproducible code snippet for us? Have you read the posting guide here? http://www.bioconductor.org/help/mailing-list/posting-guide/ What is Gga1? Is this a database you made from scratch? Did you generate it using AnnotationDbi? When you said "goProfyles " did you mean that you are actually using the goProfiles package? Assuming you are, the error you describe sounds like goProfiles is looking for a bimap object, which means you need an annotation package. If so, have you read the vignette called "SQLForge: An easy way to create a new annotation package with a standard database schema." from AnnotationDbi? You can find that here BTW: http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.h tml Marc On 11/30/2011 05:18 PM, Dana.Stanley at csiro.au wrote: > Hi all > > I am trying to use goProfyles with my custom chicken database GGal.db. The package is looking for the file in my database that does not exist : > > Error in eval(expr, envir, enclos) : object 'GGal.dbENTREZID' not found > > I can make a simple table linking my ID and entrez id that the package is looking for, but I could not figure out how to add it to the database... > To all of you reading posts and helping others a big THANKS. > > Dana > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

ADD COMMENT • link 12.4 years ago Marc Carlson ★ 7.2k

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Dana.Stanley@csiro.au ▴ 110

@danastanleycsiroau-3979

Last seen 9.6 years ago

Thanks Marc Sorry for the late reply, I was away for a week. I did use SQLForge to make a (AnnotationDbi) custom package that I called GGal.db. It works for all I need, like oligo, limma etc, but when I tried to run goProfyles package with GGal.db it was asking for the object "GGal.dbENTREZID' not found" Because it named the object starting with GGal.db I assumed that the object should be in the database, and since it was not there, I again assumed I should find a way to add it to db. I know it is looking for a file with 2 columns, my platform gene ID vs ENTREZ ID. I thought if I add this table to the sqlite database maybe it would work??? I was probably wrong. Then I thought that I should make an object in R (not in the database) and call it GGal.dbENTREZID. I tried this: >GGal.dbENTREZID=read.table("GGal.dbENTREZID.txt", header=TRUE, sep="\t") > head(GGal.dbENTREZID) ID ENTREZID 1 CLIGG_02786 373854 2 RIGG10718 373854 3 CLIGG_03262 373886 4 RIGG10181 373886 5 RIGG10182 373886 6 CLIGG_01647 373887 Then the goProfiles did not ask for the object GGal.dbENTREZID but gave me an error: Error in mget(probeslist, env = myenvir, ifnotfound = NA) : second argument must be an environment As usual I tried to google out what this means with no success. I assume I should use something other than read.table to make an object but I could not find instructions in the package. I only know basic R and the packages I need to use, I can use any help or advice in how to proceed. Thanks Dana [[alternative HTML version deleted]]

ADD COMMENT • link 12.4 years ago Dana.Stanley@csiro.au ▴ 110

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Hi Dana, If you used SQLForge, then I would expect that you have a GGa1ENTREZID object that is loaded when you load your GGa1.db package? This is probably what goProfyles is looking for. In any case the data.frame you have constructed below is probably not what the software expects. It probably expected a ProbeAnnDbBimap object (try: class(GGa1ENTREZID) ). You probably just need to make a copy of the one you have like this: GGal.dbENTREZID <- GGa1ENTREZID Which should work if I am correct about you having a GGa1ENTREZID on your search path after loading your package? Hope this helps, Marc On 12/08/2011 04:37 AM, Dana.Stanley at csiro.au wrote: > Thanks Marc > > Sorry for the late reply, I was away for a week. I did use SQLForge to make a (AnnotationDbi) custom package that I called GGal.db. It works for all I need, like oligo, limma etc, but when I tried to run goProfyles package with GGal.db it was asking for the object "GGal.dbENTREZID' not found" Because it named the object starting with GGal.db I assumed that the object should be in the database, and since it was not there, I again assumed I should find a way to add it to db. I know it is looking for a file with 2 columns, my platform gene ID vs ENTREZ ID. I thought if I add this table to the sqlite database maybe it would work??? I was probably wrong. Then I thought that I should make an object in R (not in the database) and call it GGal.dbENTREZID. I tried this: >> GGal.dbENTREZID=read.table("GGal.dbENTREZID.txt", header=TRUE, sep="\t") >> head(GGal.dbENTREZID) > ID ENTREZID > 1 CLIGG_02786 373854 > 2 RIGG10718 373854 > 3 CLIGG_03262 373886 > 4 RIGG10181 373886 > 5 RIGG10182 373886 > 6 CLIGG_01647 373887 > > Then the goProfiles did not ask for the object GGal.dbENTREZID but gave me an error: > Error in mget(probeslist, env = myenvir, ifnotfound = NA) : > second argument must be an environment > > As usual I tried to google out what this means with no success. I assume I should use something other than read.table to make an object but I could not find instructions in the package. I only know basic R and the packages I need to use, I can use any help or advice in how to proceed. > > Thanks > Dana > > [[alternative HTML version deleted]] > > _______________________________________________ > 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

ADD REPLY • link 12.4 years ago Marc Carlson ★ 7.2k

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