[BioC] an error in AnnotationForge

[James W. MacDonald]

Hi Peter,

On 4/21/2013 10:25 PM, Wang Peter wrote:
> source("http://bioconductor.org/biocLite.R");
> biocLite("human.db0");
> biocLite("AnnotationDbi");
> biocLite("AnnotationForge");
> library(human.db0);
> library(AnnotationDbi);
> library(AnnotationForge);

First, this isn't Perl, so adding in extraneous semi-colons isn't necessary.

>> available.chipdbschemas();
>> dir.create("primeview");
>>
> populateDB("HUMANCHIP_DB",affy=F,prefix="primeview",fileName="primeviewHumanGeneExprs.txt",metaDataSrc=c("DBSCHEMA"="HUMANCHIP_DB","ORGANISM"="Homo
> sapiens","SPECIES"="Human","MANUFACTURER"="Affymetrix","CHIPNAME"="PrimeView
> Human Gene Expression Array","MANUFACTURERURL"="http://www.affymetrix.com
> "),baseMapType="eg",outputDir="primeview");

You are using arguments for makeDBPackage, but calling populateDB. There 
is no reason that I can think of that you should be using populateDB 
directly, unless you just want the sqlite database. I have no idea why 
you are doing things this way - why not just follow the vignette?

In addition, about half of your arguments are all caps, and are quoted. 
There are no all caps arguments for any of the functions you are trying 
to use, nor are there any quoted arguments in R.

I would recommend just following the vignette. Also, IIRC the primeview 
chip is just a 3'-biased array, so you can probably also set affy = TRUE 
and have the parsing of the file done automatically.

Best,

Jim



>> seed<-new("AnnDbPkgSeed",Package =
> "primeview.db",Version="1.0.0",PkgTemplate="HUMANCHIP.DB",AnnObjPrefix="primeview");
> makeAnnDbPkg(seed,file.path("primeview","primeview.sqlite"),dest_dir="primeview");
> Error in match(x, table, nomatch = 0L) :
> object 'doc_template_names' not found
>> sessionInfo()
> R version 3.0.0 (2013-04-03)
> Platform: x86_64-apple-darwin10.8.0 (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] parallel stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] AnnotationForge_1.2.0 org.Hs.eg.db_2.9.0 RSQLite_0.11.3 DBI_0.2-5
> human.db0_2.9.0
> [6] AnnotationDbi_1.22.1 Biobase_2.20.0 BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.18.0 stats4_3.0.0 tools_3.0.0
>
>

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