No, there wasn't.  I should have realized the affy argument referred to the actual Affy based annotation file; that worked great.  Thanks for your help!  - Scott

From: "James W. MacDonald" <jmacdon@uw.edu<mailto:jmacdon@uw.edu>>
Date: Thursday, July 11, 2013 10:30 AM
To: "Scott Presnell [guest]" <guest@bioconductor.org<mailto:guest@bioconductor.org>>
Cc: "bioconductor@r-project.org<mailto:bioconductor@r-project.org>" <bioconductor@r-project.org<mailto:bioconductor@r-project.org>>, Scott Presnell <SPresnell@benaroyaresearch.org<mailto:SPresnell@benaroyaresearch.org>>, AnnotationForge Maintainer <maintainer@bioconductor.org<mailto:maintainer@bioconductor.org>>
Subject: Re: [BioC] MakeDBPackage fails with SQL error

Hi Scott,

Is there a particular reason you aren't using the Affy annotation file?

> makeDBPackage("HUMANCHIP_DB", affy = TRUE, prefix="primeview",
fileName="PrimeView.na32.annot.csv", baseMapType="gbNRef",outputDir=".",
version = "12.1.0", manufacturer="Affymetrix",
manufacturerUrl="http://www.affymetrix.com")
baseMapType is gb or gbNRef
Prepending Metadata
Creating Genes table
Appending Probes
Found 49372 Probe Accessions
Appending Gene Info
Found 47327 Gene Names
Found 47327 Gene Symbols
Appending Chromosomes
Appending Cytogenetic Locations
Appending Omim
Appending RefSeq
Appending Pubmed
Appending Unigene
Appending ChrLengths
Appending 3 GO tables
Appending 3 GO ALL tables
Appending KEGG
Appending EC
Appending Chromosome Locations
Appending Pfam
Appending Prosite
Appending Alias
Appending Ensembl
Appending Uniprot
Appending Metadata


simplifying probes table
dropping redundant data
Creating package in ./primeview.db

And see attached. You can install using

install.packages("primeview.db_12.1.0.tar.gz", repos=NULL, type = "source")

It won't like that you are using R-2.15.1 and it was built under
R-3.0.0, but it will just give a warning (and you should be upgrading
anyway).

Best,

Jim



On 7/10/2013 5:01 PM, Scott Presnell [guest] wrote:
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


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James W. MacDonald, M.S.
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