Entering edit mode
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
