[BioC] problem using annotation database with annaffy

Georg Otto georg.otto at tuebingen.mpg.de
Tue May 19 19:46:37 CEST 2009


I built an annotation package for the Agilent zebrafish array and used
this in combination with annaffy to generate text files and html with
expression data and annotations. This used to work fine before I upgraded to
R 2.9 and bioconductor 2.4. Now, i get an error:

> library(annaffy)
> library(limma)
> library(zebrafishAG.db, lib.loc="~/rlib")

> probeids<-as.character(fit$genes$ID)

> length(probeids)
[1] 45220

>  table<-aafGO(probeids, chip="zebrafishAG.db")
Error in sqliteExecStatement(con, statement, bind.data) : 
  RS-DBI driver: (error in statement: String or BLOB exceeded size limit)

See also the output from traceback() below

Has the GO data become so much bigger in the last upgrade, so it exceeds
a size limit now? Or are there other incompatibilities? It works with
probeids[1:30000] and probeids[10000:length(probeids)], so I think the
size is the issue (as the error message says), not a faulty probeid

On the other side, it works with PubMed:

>  table<-aafPubMed(probeids, chip="zebrafishAG.db")

So it must have to do with the size and the structure of the GO data.

Any idea how to fix this?



> traceback()
6: .Call("RS_SQLite_exec", conId, statement, bind.data, PACKAGE = .SQLitePkgName)
5: sqliteExecStatement(con, statement, bind.data)
4: sqliteQuickSQL(conn, statement, ...)
3: dbGetQuery(dbconn, dbquery)
2: dbGetQuery(dbconn, dbquery)
1: aafGO(probeids, chip = "zebrafishAG.db")
> sessionInfo()
R version 2.9.0 (2009-04-17) 


attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] zebrafishAG.db_2.2.11 limma_2.18.0          annaffy_1.16.0       
[4] KEGG.db_2.2.5         GO.db_2.2.11          RSQLite_0.7-1        
[7] DBI_0.2-4             AnnotationDbi_1.6.0   Biobase_2.4.1        

loaded via a namespace (and not attached):
[1] tools_2.9.0

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