[BioC] Error using makeDBPackage() from AnnotationForge package

[Marc Carlson]

Hi Gabriel,

I am confused about why you are posting this?  Did you not see Jims 
response yesterday?  The one in which he responded to having already 
responded to the identical question posted earlier?  I feel sudden 
concern that we have somehow gotten stuck in some sort of recursive 
mailing list question...  ;)

Here is where it stood as of yesterday:

https://stat.ethz.ch/pipermail/bioconductor/2013-September/054891.html


If it's really important that you use your own file, could you please 
send it to me so that I can have a look at it?


   Marc



On 09/13/2013 04:06 AM, Gabriel Teku wrote:
> Hi bioc,
> I'm having trouble with the problem of creating the annotation package for
> organism = human, array type = custom array, and I it'll really be nice to
> get some help at this point.
> Here is what I've done so far without success:
> -- I've followed the instructions given in the AnnotationForge package
> vignettes titled "SQLForge: An easy way to create a new annotation package
> with a standard database schema."
> -- First, I created the probe --> entrezgene id mapping for the custom
> array
> -- Re-installed the org.Hs.eg.db package
> -- Run the makeDBPackage function, which fails
> Here is the code snippet
>
>> head(hcg3278_ID) # table of probe --> entrez id mapping  probe_id entregene_id
> 1  19249_1       153579
> 2  19251_1        53335
> 3  19253_1         3603
> 4  19255_1         6004
> 5  19257_1       115350
> 6  23809_1       729082> write.table(hcg3278_ID, file="hcg3278_ID",
> sep="\t", row=F, col=F)
>
>> makeDBPackage(schema = "HUMANCHIP_DB", affy=F, pref="hcg3278", fileName="hcg3278_ID", baseMapType="eg", version="1.0.0", manufacturer="The Staudt laboratory", chipName="NCI/Staudt human 15K v13", outputDir = getwd())
> baseMapType is eg
> Prepending MetadataCreating Genes tableError in
> sqliteExecStatement(con, statement, bind.data) :
>    RS-DBI driver: (RS_SQLite_exec: could not execute1: genes.gene_id
> may not be NULL)
>
>
>> sessionInfo()R version 3.0.1 (2013-05-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
> LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
> LC_MONETARY=en_US.UTF-8
>   [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=C                 LC_NAME=C
>                 LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets
> methods   base
>
> other attached packages:
> [1] AnnotationForge_1.2.2 org.Hs.eg.db_2.9.0    RSQLite_0.11.4
> DBI_0.2-7             AnnotationDbi_1.22.6  Biobase_2.20.1
> [7] BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
> [1] data.table_1.8.10 IRanges_1.18.3    plyr_1.8          stats4_3.0.1
>       tools_3.0.1
>
>
> Thanks in advance
>
>
> Gabriel Teku
>
> 	[[alternative HTML version deleted]]
>
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