Hello. I'm trying to build a annotation package for a custom printed array. I'm running the code.....: library(AnnotationDbi) setwd("/Users/marcusgry/Desktop/bygga mus.annot") Infile <- "/Users/marcusgry/Desktop/bygga mus.annot/alla.gb.txt" OutDir <- "/Users/marcusgry/Desktop/bygga mus.annot" makeMOUSECHIP_DB(affy=FALSE, prefix="KTH.mmOligo", fileName=Infile, baseMapType="gb",outputDir = OutDir,version="1.0.1",manufacturer = "KTH",chipName = "KTH Whole Genome Oligo Chip",manufacturerUrl = "http://www.ktharray.com ") And the response is: "baseMapType is gb or gbNRef Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: no such table: src.accession)" The input file is a file which looks like: Mouse_v401D01 M28821;BC145741 Mouse_v401H01 AK148357 ;AK014619 ;BC079678 ;X51743 ;D00439 ;M26729 ;M24560 ;M20234 ;X12782 ;D00131;D00440;AY012001;AK148432;AK148172;AK148341;CH466543;AY526904 Mouse_v401L01 AK010225;X99251 ...and so forth. I am using macOSX, version 10.5.6, and R-version 2.8.1. The AnnotationDbi is version 1.4.2. Do anyone know what the problem might be? I would really appreciate all the help that I can get. Yours sincerely Marcus [[alternative HTML version deleted]]

Hi Marcus, Did you install the mouse.db0 package 1st? You might also want to have a look at the SQLForge vignette in the AnnotationDbi package if you have not found it already: http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.htm l Marc Marcus Gry wrote: > Hello. > > I'm trying to build a annotation package for a custom printed array. > > I'm running the code.....: > library(AnnotationDbi) > setwd("/Users/marcusgry/Desktop/bygga mus.annot") > Infile <- "/Users/marcusgry/Desktop/bygga mus.annot/alla.gb.txt" > OutDir <- "/Users/marcusgry/Desktop/bygga mus.annot" > > makeMOUSECHIP_DB(affy=FALSE, prefix="KTH.mmOligo", fileName=Infile, > baseMapType="gb",outputDir = OutDir,version="1.0.1",manufacturer = > "KTH",chipName = "KTH Whole Genome Oligo Chip",manufacturerUrl = "http://www.ktharray.com > ") > > > And the response is: > > "baseMapType is gb or gbNRef > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (error in statement: no such table: src.accession)" > > The input file is a file which looks like: > > Mouse_v401D01 M28821;BC145741 > Mouse_v401H01 > AK148357 > ;AK014619 > ;BC079678 > ;X51743 > ;D00439 > ;M26729 > ;M24560 > ;M20234 > ;X12782 > ;D00131;D00440;AY012001;AK148432;AK148172;AK148341;CH466543;AY526904 > Mouse_v401L01 AK010225;X99251 > > ...and so forth. > > I am using macOSX, version 10.5.6, and R-version 2.8.1. The > AnnotationDbi is version 1.4.2. > > > Do anyone know what the problem might be? > > I would really appreciate all the help that I can get. > > > Yours sincerely > > Marcus > > > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 > >