[BioC] MakeDBPackage fails with SQL error
James W. MacDonald
jmacdon at uw.edu
Wed Sep 11 15:52:18 CEST 2013
You seem to have found Scott Presnell's original email, but not my
On Wednesday, September 11, 2013 5:53:15 AM, Gabriel wrote:
> 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:
>>> tmpout = tempdir()
>> prefix="primeview", fileName="primeviewHumanGeneExprs2.txt",
>> outputDir = tmpout,
>> 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():
>> R version 2.15.2 (2012-10-26)
>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>> attached base packages:
>>  stats graphics grDevices utils datasets methods base
>> other attached packages:
>>  human.db0_2.8.0 AnnotationForge_1.0.3 org.Hs.eg.db_2.8.0
>>  RSQLite_0.11.2 DBI_0.2-5 AnnotationDbi_1.20.7
>>  Biobase_2.18.0 BiocGenerics_0.4.0
>> loaded via a namespace (and not attached):
>>  IRanges_1.16.6 parallel_2.15.2 stats4_2.15.2
>> Sent via the guest posting facility at bioconductor.org.
>> Bioconductor mailing list
>> Bioconductor at ...
>> Search the archives:
> 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.
> Bioconductor mailing list
> Bioconductor at r-project.org
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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