Question: problem using annotation database with annaffy
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gravatar for Georg Otto
10.0 years ago by
Georg Otto510
Georg Otto510 wrote:
Hi, 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 entry. 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? Cheers, Georg > 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) x86_64-redhat-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C 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
annotation go zebrafish annaffy • 452 views
ADD COMMENTlink written 10.0 years ago by Georg Otto510
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