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

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