[BioC] MakeDBPackage fails with SQL error

[James W. MacDonald]

Hi Gabriel,

You seem to have found Scott Presnell's original email, but not my 
response:

https://stat.ethz.ch/pipermail/bioconductor/attachments/20130711/7e4d77fb/attachment.pl

Best,

Jim



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:
>>
>>> 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
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099