Question: ABPkgBuilder question
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gravatar for Kamila Naxerova
11.1 years ago by
Kamila Naxerova40 wrote:
Hi all, I am - not very successfully - playing with AnnBuilder and would appreciate any comments on the error I am getting (system info below). Confusingly, the same code *seems* to work fine on my windows machine, only here I don't want to deal with unzipping problems. Sorry if this is something obvious. platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 7.1 year 2008 month 06 day 23 svn rev 45970 language R library(hgu133plus2.db) x=hgu133plus2ENTREZID xx=as.list(x) basefile=data.frame(names(xx),as.character(unlist(xx))) write.table(basefile,"Basefile.txt",sep="\t",row.names=F) library(AnnBuilder) mySrcUrls=getSrcUrl("all",organism="Homo sapiens") ABPkgBuilder(baseName = read.table("Basefile.txt",header=F,sep="\t"), srcUrls = mySrcUrls, baseMapType ="ll", pkgName = "hgu133plus2", pkgPath = getwd(), organism = "Homo sapiens", version = "1.1.0",author = list(authors = "K"),fromWeb=TRUE) Error in validObject(.Object) : invalid class "UG" object: invalid object for slot "baseFile" in class "UG": got class "data.frame", should be or extend class "character" Calls: ABPkgBuilder ... UG -> new -> initialize -> initialize -> validObject Execution halted Thanks, Kamila
organism annbuilder • 564 views
ADD COMMENTlink modified 11.1 years ago by Marc Carlson7.2k • written 11.1 years ago by Kamila Naxerova40
Answer: ABPkgBuilder question
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gravatar for Marc Carlson
11.1 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Kamila Naxerova wrote: > Hi all, > > I am - not very successfully - playing with AnnBuilder and would > appreciate any comments on the error I am getting (system info below). > Confusingly, the same code *seems* to work fine on my windows machine, > only here I don't want to deal with unzipping problems. Sorry if this is > something obvious. > > platform x86_64-unknown-linux-gnu > arch x86_64 > os linux-gnu > system x86_64, linux-gnu > status > major 2 > minor 7.1 > year 2008 > month 06 > day 23 > svn rev 45970 > language R > > > library(hgu133plus2.db) > x=hgu133plus2ENTREZID > xx=as.list(x) > basefile=data.frame(names(xx),as.character(unlist(xx))) > write.table(basefile,"Basefile.txt",sep="\t",row.names=F) > > library(AnnBuilder) > mySrcUrls=getSrcUrl("all",organism="Homo sapiens") > > ABPkgBuilder(baseName = read.table("Basefile.txt",header=F,sep="\t"), > srcUrls = mySrcUrls, baseMapType ="ll", pkgName = "hgu133plus2", > pkgPath = getwd(), organism = "Homo sapiens", version = "1.1.0",author = > list(authors = "K"),fromWeb=TRUE) > > Error in validObject(.Object) : > invalid class "UG" object: invalid object for slot "baseFile" in class > "UG": got class "data.frame", should be or extend class "character" > Calls: ABPkgBuilder ... UG -> new -> initialize -> initialize -> validObject > Execution halted > > > Thanks, > Kamila > Hi Kamila, It looks like you might be trying to make a customized annotation package for human? If so, then instead of AnnBuilder, please use the SQLForge functions inside of AnnotationDbi to make custom annotation packages. This will allow you to make a more modern ".db" style annotation package. You can find the instructions here: http://www.bioconductor.org/packages/2.3/bioc/html/AnnotationDbi.html If you have further questions, please feel free to ask, Marc
ADD COMMENTlink written 11.1 years ago by Marc Carlson7.2k
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