[BioC] AnnotationDBI

[James W. MacDonald]

Hi Nick,

On 9/26/2012 11:42 AM, Nick Burgoyne [guest] wrote:
> Hi all,
>
> I am contacting you regarding a problem with the AnnotationDBI package.
>
> I am trying to generate my own database from Agilent chips (surprise, surprise, problems with these again), and keep running into the same problem.
>
> Any advice would be very welcome!
>
> I have created an input (test.txt) but it really doesn’t matter how long or weather I select for refseq or genbank entries.
>
> Everything seems up to date, and no matter what input, the same error occurs.
>
> Don’t hate me, I’ve no choice, but is it because I use windows?

Ugh. These nasty windows people... ;-D

>
> test.txt
> ########################
> A_24_P66027	NM_00490
> A_23_P212522	NM_01461
> A_24_P9671	NM_001539
> A_24_P801451	NM_006709
> A_32_P30710	NM_000978
> ########################
>
> I am calling:
> ########################
> makeDBPackage(“HUMANCHIP_DB”,
> 	affy = FALSE,
> 	prefix = "test",
> 	fileName = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\test.txt",
> 	baseMapType = "refseq",
> 	outputDir = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\",

Here is a stab in the dark. If you notice below, there is a 
paste(outputdir, "/", prefix, ".sqlite"), which will result in

C:\\Users\\np221\\BioinfWork\\AgilentRDatabases\\/test.sqlite

Which might result in a problem. Note that R on windows will happily use 
forward slashes, so you could change outputDir to 
C:/Users/nb221/BioinfWork/AgilentRdatabases. I would personally omit the 
trailing forward slash, but in my experience I haven't seen too much 
backlash if one is used (and you end up with double forward slashes in 
your file path).

In addition, you need to include an author and maintainer field, and the 
maintainer field has to be something like "Me <me at mine.com>" or when you 
try to build/check/install R will fail with a complaint about a 
misformed field in your DESCRIPTION file.

Best,

Jim


> 	version = "1.0.0",
> 	manufacturer = "Agilent",
> 	chipName = "test",
> 	manufacturerUrl = "http://www.agilent.com")
> ########################
>
> Getting the output:
> ########################
> Loading required package: RSQLite
> Loading required package: DBI
> baseMapType is refseq
> Prepending Metadata
> Creating Genes table
> Appending Probes
> Found 5 Probe Accessions
> Appending Gene Info
> Found 3 Gene Names
> Found 3 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
> Error in makeAnnDbPkg(seed, paste(outputDir, "/", prefix, ".sqlite", sep = ""),  :
>    subscript out of bounds
> ########################
>
> ########################
>> traceback()
> 4: makeAnnDbPkg(seed, paste(outputDir, "/", prefix, ".sqlite", sep = ""),
>         dest_dir = outputDir)
> 3: makeAnnDbPkg(seed, paste(outputDir, "/", prefix, ".sqlite", sep = ""),
>         dest_dir = outputDir)
> 2: AnnotationDbi:::.makeHUMANCHIP_DB(...)
> 1: makeDBPackage(“HUMANCHIP_DB”, affy = FALSE, prefix = "test", fileName = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\test.txt",
>         baseMapType = "refseq", outputDir = "C:\\Users\\nb221\\BioinfWork\\AgilentRDatabases\\",
>         version = "1.0.0", manufacturer = "Agilent", chipName = "test",
>         manufacturerUrl = "http://www.agilent.com")
> #########################
>
> Many thanks,
>
> Nick Burgoyne
>
>
>   -- output of sessionInfo():
>
> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252
> [2] LC_CTYPE=English_United Kingdom.1252
> [3] LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] RSQLite_0.11.2       DBI_0.2-5            limma_3.12.3
> [4] AnnotationDbi_1.18.3 Biobase_2.16.0       BiocGenerics_0.2.0
> [7] BiocInstaller_1.4.7
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.14.4 stats4_2.15.1  tools_2.15.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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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