[BioC] AnnotationDbi problem.

[Marc Carlson]

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.html


  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
>
>
>
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>
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