[BioC] AnnotationDBI

[Nick Burgoyne [guest]]

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?

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\\",
	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.