[BioC] MakeDBPackage fails with SQL error

[Gabriel]

Scott Presnell [guest] <guest at ...> writes:

> 
> 
> Hi Folks,
>   I've been trying to create a DB package for the Affymetrix Primeview 
micro array chip.  I found the vignette
> called 'Creating a New Annotation Package using SQLForge'  I created a 
mapping of probes to entrez gene
> ids.  And I installed the requisite packages.  And ran the following:
> 
> > library(AnnotationForge)
> > library("human.db0")
> > tmpout = tempdir()
> > makeDBPackage("HUMANCHIP_DB",
> affy=FALSE,
> prefix="primeview", fileName="primeviewHumanGeneExprs2.txt",
> baseMapType="gb",
> outputDir = tmpout,
> version="1.0.0",
> manufacturer = "Affymetrix",
> chipName="Primeview MicroArray",
> manufacturerUrl = "http://www.affymetrix.com")
> baseMapType is gb or gbNRef
> Prepending Metadata
> Creating Genes table
> Error in sqliteExecStatement(con, statement, bind.data) : 
>   RS-DBI driver: (RS_SQLite_exec: could not execute1: genes.gene_id may 
not be NULL)
> 
> But as you can see, I get an SQL based error.  Thinking it was complaining 
about probes that don't have a
> corresponding entrez gene Id, I removed them from the file (they 
originally had a '---' as an entrez gene
> id), and tried again, but the result is the same.
> 
> Can someone provide me with some guidance on where to look to fix or avoid 
this error?
> 
> (alternatively, if anyone is willing to share a primeview.db package, that 
would also be great!)
> 
>  -- output of sessionInfo(): 
> 
> > sessionInfo();
> R version 2.15.2 (2012-10-26)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (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] stats     graphics  grDevices utils     datasets  methods   base     
> 
> other attached packages:
> [1] human.db0_2.8.0       AnnotationForge_1.0.3 org.Hs.eg.db_2.8.0   
> [4] RSQLite_0.11.2        DBI_0.2-5             AnnotationDbi_1.20.7 
> [7] Biobase_2.18.0        BiocGenerics_0.4.0   
> 
> loaded via a namespace (and not attached):
> [1] IRanges_1.16.6  parallel_2.15.2 stats4_2.15.2  
> 
> --
> Sent via the guest posting facility at bioconductor.org.
> 
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> 

Hi Scott,
I'm having a similar issue and suspect that the error is as a result of some
of the gene ids in the probe-to-id fileName don't have a corresponding gene
mapping behind the scene.
May be track down those gene ids and eliminating them would solve the issue.
I'll report what I find. In the mean time, it would nice to hear from others
about this issue.

Gabriel